This study aims to conduct a comparative analysis of the quality and flavor of meat from four categories of Mongolian horses (Wushen, Baicha, Barhu, and Ujimqin). Physicochemical indicators, electronic nose, electronic tongue, and lipidomics were used to characterize meat quality and flavor and to screen for differential markers. Results showed that Wushen Horses had the highest pH_45min, serine, glutamic acid, total free amino acids (∑FAA), total non-essential amino acids (∑NEAA), total amino acids (∑TAA), NEAA/TAA, W2S sensor response, umami and richness values, and had the lowest cooking loss, EAA/TAA, EAA/NEAA, sourness, bitterness and aftertaste B values (p < 0.01). In contrast, Barhu Horses had the highest b*_45min, C20:2 and saltiness values, and had the lowest W5S, W1S and W2W sensor responses (p < 0.01). Lipidomics identified 163 differential lipids (DELs) as potential markers, including LPC (18:2/0:0) and PC (16:0_16:0). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed DELs were significantly enriched in glycerolipid, linoleic acid, arachidonic acid and α-linolenic acid metabolism pathways. Correlation analysis indicated 23 DELs (e.g., carnitine C20:4) correlated positively with umami, W2S and richness, but negatively with shear force and cooking loss. In summary, our data show that among the four categories of Mongolian horses, Wushen Horses exhibited the best meat quality and flavor, while Barhu Horses showed the poorest. The differences in meat quality and flavor were closely associated with changes in lipid composition. This study provides direct molecular evidence from lipids for the variation in meat quality among Mongolian horses.

Horse meat is a high-quality protein source. A total of 50 two-year-old male horses with similar body weights (300 ± 50 kg) were used: 30 for regional comparison (10 each from Bulgan province region of Mongolia (BPM), Tuv province region of Mongolia (TPM), and Inner Mongolia region of China (IMC)) and an additional 20 from the IMC region for muscle-site analysis. To elucidate the molecular mechanisms underlying regional and muscle-site differences in the meat quality of Mongolian horses, with particular emphasis on tenderness, this study analyzed chemical composition, minerals, fatty acids, and transcriptomes. Results showed that Mongolian horses from the Inner Mongolia region of China (IMC) had the highest contents of Se, C17:1, C18:2n6c, C18:3n3, ∑PUFA, PUFA/SFA, ∑n-3PUFA, ∑n-6PUFA (p < 0.05), and Fe (p < 0.01), and the lowest levels of C15:0 (p < 0.01) and C16:0 (p < 0.05). The Mongolian horses from the Tuv province region of Mongolia (TPM) had the highest Ca content (p < 0.05). The Mongolian horses from the Bulgan province region of Mongolia (BPM) had the highest ∑SFA (p < 0.01). The forelimb (FL) had the highest a*_45min, b*_45min (p < 0.01), Fe, Zn, and C17:1 (p < 0.05), and the lowest shear force and drip loss (p < 0.01). The HD had the highest pH_45min and cooking loss (p < 0.01). The hindlimb (HD) increased the L*_45min compared with the FL (p < 0.01). Transcriptomic analysis identified 513 differentially expressed genes (DEGs) between FL and HD, including SLC16A7, GPAM, FABP3, and TNNC1. KEGG enrichment analysis revealed that these DEGs were significantly enriched in the cGMP-PKG signaling pathway, glycerophospholipid metabolism, and PPAR signaling pathway. In summary, this study demonstrated that among Mongolian horses from three different regions, IMC horses exhibited superior meat quality and flavor characteristics, and the FL of IMC horses showed significantly better meat quality than other anatomical sites. Transcriptomic analysis identified a set of candidate genes related to meat quality and lipid metabolism, including SLC16A7, GPAM, FABP3, and TNNC1, providing a scientific basis for further understanding of muscle-specific molecular mechanisms in Mongolian horses. Furthermore, the observed differences in physicochemical and nutritional properties across regions and muscle sites established a systematic foundation for quality grading, targeted nutritional utilization, and processing optimization of Mongolian horse meat.