Genomic structural variation (SV) refers to differences in gene sequences between individuals on a genomic scale. It is widely distributed in the genome, primarily in the form of insertions, deletions, duplications, inversions, and translocations. Due to its characterization by long segments and large coverage, SVs significantly impact the genetic characteristics and production performance of livestock, playing a crucial role in studying breed diversity, biological evolution, and disease correlation. Research on SVs contributes to an enhanced understanding of chromosome function and genetic characteristics and is important for understanding hereditary diseases mechanisms. In this article, we review the concept, classification, main formation mechanisms, detection methods, and advancement of research on SVs in the genomes of cattle, buffalo, equine, sheep, and goats, aiming to reveal the genetic basis of differences in phenotypic traits and adaptive genetic mechanisms through genomic research, which will provide a theoretical basis for better understanding and utilizing the genetic resources of herbivorous livestock.

Herbivorous livestock, such as cattle, sheep, goats, horses, and donkeys, play a crucial role in agricultural production and possess remarkable resilience to extreme environmental conditions, driven by complex genetic mechanisms. Recent advancements in high-throughput sequencing, genome assembly, and environmental data integration have enabled a deeper understanding of the genetic basis of their environmental adaptation. This review identifies key genes associated with high-altitude, heat, cold, and drought adaptation, providing insights into the molecular mechanisms underlying these traits. By elucidating these genetic adaptations, our study aims to support conservation efforts, inform selective breeding programs, and enhance agricultural productivity, ultimately contributing to sustainable livestock farming and economic benefits for farmers.

Variation in coat color among equids has attracted significant interest in genetics and breeding research. The range of colors is primarily determined by the type, concentration, and distribution of melanin pigments, with the balance between eumelanin and pheomelanin influenced by numerous genetic factors. Advances in genomic and sequencing technologies have enabled the identification of several candidate genes that influence coat color, thereby clarifying the genetic basis of these diverse phenotypes. In this review, we concisely categorize coat coloration in horses and donkeys, focusing on the biosynthesis and types of melanin involved in pigmentation. Moreover, we highlight the regulatory roles of some key candidate genes, such as MC1R, TYR, MITF, ASIP, and KIT, in coat color variation. Moreover, the review explores how coat color relates to selective breeding and specific equine diseases, offering valuable insights for developing breeding strategies that enhance both the esthetic and health aspects of equine species.

DNA methylation represents a predominant epigenetic modification with broad implications in various biological functions. Its role is particularly significant in the process of collagen deposition, a fundamental aspect of dermal development in donkeys. Despite its critical involvement, the mechanistic insights into how DNA methylation influences collagen deposition in donkey skin remain limited. In this study, we employed whole genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) to investigate the epigenetic landscape and gene expression profiles in the dorsal skin tissues of Dezhou donkeys across three developmental stages: embryonic (YD), juvenile (2-year-old, MD), and mature (8-year-old, OD). Our analysis identified numerous differentially methylated genes that play pivotal roles in skin collagen deposition and overall skin maturation, including but not limited to COL1A1, COL1A2, COL3A1, COL4A1, COL4A2, GLUL, SFRP2, FOSL1, SERPINE1, MMP1, MMP2, MMP9, and MMP13. Notably, we observed an inverse relationship between gene expression and DNA methylation proximal to transcription start sites (TSSs), whereas a direct correlation was detected in regions close to transcription termination sites (TTSs). Detailed bisulfite sequencing analyses of the COL1A1 promoter region revealed a low methylation status during the embryonic stage, correlating with elevated transcriptional activity and gene expression levels. Collectively, our findings elucidate key genetic markers associated with collagen deposition in the skin of Dezhou donkeys, underscoring the significant regulatory role of DNA methylation. This research work contributes to the foundational knowledge necessary for the genetic improvement and selective breeding of Dezhou donkeys, aiming to enhance skin quality attributes.

This review comprehensively examines the molecular basis of donkey meat characteristics and growth-associated genes, integrating findings from multiple omics approaches. This study examines the nutritional profile of donkey meat, which is rich in protein, essential amino acids, and unsaturated fatty acids. Through a systematic literature search across Web of Science, Google Scholar, PubMed, and Scopus databases (2000–2024), we collected and analyzed data from 400 research articles using predefined inclusion criteria focused on nutritional composition, omics approaches, and meat quality parameters in donkey populations. The study also evaluates various factors affecting meat quality, including breed differences, age, feeding management, and storage conditions. Advanced genomic and transcriptomic analyses have revealed numerous candidate genes, such as ACTN3, BMP7, NR6A1, Wnt7a, HOXC8, LCORL, TPM2, and TPM3, associated with growth traits and meat quality characteristics, providing valuable insights for genetic improvement programs. Furthermore, the review discusses various authentication methods for ensuring donkey meat quality and preventing adulteration, highlighting the integration of traditional and modern analytical approaches.

The donkey (Equus asinus), despite its long domestication history, has often been overlooked and is currently facing the dual challenge of genetic erosion and emerging economic opportunities. Global research indicates that although Chinese indigenous breeds maintain a moderate level of genetic diversity, the rapid transition from draft purposes to large-scale ejiao production has driven them into severe endangerment, leading to a dramatic decline in donkey population. In contrast, donkey populations in Europe and the Mediterranean, though numerically smaller, have achieved greater stability through conservation programs and integration into specialized sectors such as dairy production and tourism. Genomic studies further reveal region-specific selection for traits associated with body size, adaptability, and productivity, underscoring the profound influence of ecological and management contexts. This review systematically compares Chinese and international donkey breeds in terms of genetic resources, genetic characteristics, phenotypic and reproductive traits, adaptive capacity, and industrial utilization models, with the aim of providing a foundation for global strategies in genetic conservation and sustainable development.