Animal genotyping by means of genome-wide association studies is important for connecting phenotypes of interest with their underlying genetics in livestock. However, the use of whole genome sequencing to investigate chest circumference (CC) in donkeys has rarely been reported. We aimed to use the genome-wide association study approach to detect significant single nucleotide polymorphisms (SNPs) and key genes associated with chest circumference traits in Xinjiang donkeys. We assessed 112 Xinjiang donkeys in this study. The chest circumference of each was measured 2 h before milking. We re-sequenced blood samples from the Xinjiang donkeys, and genome-wide association study analyses were performed using a mixed model with the PLINK, GEMMA, and REGENIE programs. We tested 38 donkeys for candidate SNPs for genome-wide association study using three software programs. Additionally, 18 SNP markers reached genome-wide significance (p < 1.61 × 10⁻⁹). On the basis of these, 41 genes were identified. Previously proposed candidate genes for CC traits were supported by this study, including NFATC2 (Nuclear Factor of Activated T Cells 2), PROP1 (PROP Paired-Like Homeobox 1), UBB (Ubiquitin B), and HAND2 (Heart and Neural Crest Derivatives Expressed 2). These promising candidates provide a valuable resource for validating potential meat production genes and will facilitate the development of high-yielding Xinjiang donkey breeds through marker-assisted selection or gene editing.

H3K4me3, a well-established histone modification associated with active promoters, plays a critical role in orchestrating gene expression programs that govern mammary gland development and lactation. In this study, we present the first comprehensive epigenomic profiling of H3K4me3 modifications during mammary gland development in Yili horses using Cleavage Under Targets and Tagmentation (CUT&Tag) and RNA sequencing. Mammary gland tissues were collected from two developmental stages—early lactation and peak lactation. A total of 393 differentially expressed genes (DEGs) were identified between two groups, among which 72 DEGs (54 upregulated H3K4me3 targets and 18 downregulated targets) were directly regulated by H3K4me3. KEGG enrichment analyses revealed that these DEGs were involved in ECM–receptor interaction, focal adhesion, the PI3K-Akt signaling pathway, and the calcium signaling pathway. In these pathways, five genes were identified as potential regulators of mammary gland development. Among these, PTGES, COL1A1, PDGFRB, and RYR1 exhibited consistent upregulation at both the transcriptomic and chromatin levels, whereas PRKAG3 showed significant downregulation. These findings offer novel insights into the epigenetic regulation of lactation in horses and lay a theoretical foundation for improving milk production traits through targeted molecular breeding strategies.

This study investigates the mechanisms underlying drought adaptability in Duolang sheep, a local breed from two distinct habitats in Xinjiang—an arid southern region and a grassland northern region—aiming to identify key factors driving differential environmental adaptation. Integrated multi-omics analyses were performed, including serum biochemical assays, untargeted metabolomics of perirenal and tail fat tissues, and transcriptomic profiling of lung, liver, and kidney samples. Our results revealed notable differences: (1) serum levels of GSH-Px, IL-2, and IgG were significantly higher in the southern group (p < 0.01); (2) metabolomic analysis identified key differential metabolites, including EPA (involved in unsaturated fatty acid biosynthesis), choline (glycerophospholipid metabolism), L-serine and glutathione (cofactor biosynthesis), and taurine (sulfur metabolism); and (3) transcriptomic analysis revealed significant differential expression of genes such as FGF21 (thermogenesis), CD14 and DUSP2 (MAPK signaling pathway), GOT1 (arginine biosynthesis), and AVPR2 (vasopressin-regulated water reabsorption). Integrative correlation analysis further indicated that glutathione, EPA, GOT1, and CD14 are involved in energy and lipid metabolism, while taurine, AVPR2, and DUSP2 contribute to oxidative stress resistance and immune regulation. These molecular and metabolic adjustments collectively enhance drought adaptability in southern Xinjiang Duolang sheep. In conclusion, adaptation to arid environments requires enhanced antioxidant capacity and immune function, with metabolites such as EPA supporting lipid metabolism and genes such as FGF21 regulating fatty acid oxidation to limit triglyceride accumulation.

4-Alkyl branched-chain fatty acids (BCFAs), including 4-methyloctanoic acid (4-MOA), 4-ethyloctanoic acid (4-EOA), and 4-methylnonanoic acid (4-MNA), are important contributors to the characteristic odor of sheep meat. Their concentrations and composition are closely related to meat flavor quality and consumer acceptance. Understanding the mechanisms that regulate BCFA formation and accumulation is therefore important for improving sheep meat flavor. In this study, the concentrations of these three BCFAs were measured in muscle samples from Altay (ALT), Turpan (TLF), Inner Mongolian (NM), Tan, and Hu sheep. Untargeted muscle metabolomic data from ALT and TLF sheep were integrated with publicly available datasets, including metabolomic data from Tan sheep under different feeding conditions and transcriptomic and metabolomic data from Hu and Zang sheep. These datasets were used to investigate BCFA-related metabolic networks and candidate regulatory factors associated with ecological environment, nutritional conditions, and genetic background. The results show clear differences in BCFA accumulation among the sheep populations. All three BCFAs were below the limits of detection in ALT, TLF and NM sheep. Both 4-MOA and 4-EOA were detected in Tan sheep, whereas all three BCFAs were detected in Hu sheep. The concentrations of 4-MOA and 4-EOA in Hu sheep were approximately 14.4- and 12.5-fold higher than those in Tan sheep, respectively (p < 0.001). Multi-omics integration showed that BCFA-related metabolic variation was mainly associated with branched-chain amino acid metabolism, short-chain carbon metabolism, the tricarboxylic acid (TCA) cycle, and lipid metabolism. MMUT, ACAT1, and EHHADH were identified as candidate regulatory genes. These genes are involved in methylmalonyl-CoA conversion, acetyl-CoA/acetoacetyl-CoA metabolism, and fatty acid β-oxidation, respectively. Changes in energy demand, substrate utilization, and precursor availability may alter the partitioning of BCFA precursor carbon between central energy metabolism and lipid metabolism, thereby affecting BCFA formation and accumulation. In summary, MMUT, ACAT1, and EHHADH may influence the formation and accumulation of 4-MOA, 4-EOA, and 4-MNA by regulating key metabolic reactions and carbon partitioning between the TCA cycle and lipid metabolism. Ecological environment and dietary conditions may further contribute to this process by modifying energy metabolism and precursor substrate supply. These findings provide a theoretical basis for understanding BCFA-related flavor formation and for improving sheep meat flavor through genetic selection and nutritional regulation.

Breed-associated differences in roasted-lamb flavour are often described from volatile profiles alone, whereas the links among lipid precursors, volatile abundance and olfactory activity remain less clear. Here, fatty acid profiling, headspace solid-phase microextraction–gas chromatography–mass spectrometry (HS-SPME–GC–MS) and gas chromatography–olfactometry–mass spectrometry (GC–O–MS) were combined to compare eight Chinese sheep breeds under standardised roasting conditions, although rearing conditions differed among groups. Major unsaturated fatty acids, particularly C18:1n-9, C18:2n-6, C18:3n-3 and C20:4n-6, differed markedly among breeds. Aldehydes and pyrazines dominated the roasted volatilome, but their relative contributions varied. GC–O–MS revealed a shared roasted/nutty aroma backbone, with 2,3-dimethylpyrazine detected across all breeds, whereas lipid-derived odorants including hexanal, nonanal, octanal, (E)-2-octenal and 1-octen-3-ol showed greater breed-associated variation. Some breeds exhibited pyrazine-dominant profiles, whereas others showed greater contributions from lipid-derived aldehydes and alcohols. Unsaturated fatty acids were more closely associated with lipid-derived volatiles than with pyrazines. These findings indicate that breed-associated differences in roasted-lamb aroma are characterised mainly by shifts in the relative contribution of lipid oxidation products and Maillard-derived odorants against a shared aroma-active background.

Breed-associated differences in roasted lamb flavour are often described from volatile profiles alone, whereas the links among lipid precursors, volatile abundance and olfactory activity remain less clear. Here, fatty acid profiling, headspace solid-phase microextraction–gas chromatography–mass spectrometry (HS-SPME–GC–MS) and gas chromatography–olfactometry–mass spectrometry (GC–O–MS) were combined to compare eight Chinese sheep breeds under standardized roasting conditions. Major unsaturated fatty acids, particularly C18:1, C18:2n-6, C18:3n-3 and C20:4n-6, differed markedly among breeds. Aldehydes and pyrazines dominated the roasted volatilome, but their relative contributions varied. GC–O–MS revealed a shared roasted/nutty aroma backbone, with 2,3-dimethylpyrazine detected across all breeds, whereas lipid-derived odorants including hexanal, nonanal, octanal, (E)-2-octenal and 1-octen-3-ol showed greater breed-associated variation. Some breeds exhibited pyrazine-dominant profiles, whereas others showed greater contributions from lipid-derived aldehydes and alcohols. Unsaturated fatty acids were more closely associated with lipid-derived volatiles than with pyrazines. These findings indicate that breed-associated differences in roasted lamb aroma are characterised mainly by shifts in the relative contribution of lipid oxidation products and Maillard-derived odorants against a shared aroma-active background.