Aims Yak is a dominant ruminant, well-adapted to grazing on pasture year around in the harsh climate of the 3,000-meter-high Qinghai-Tibetan Plateau. The complex microbial community that resides within the yak rumen is responsible for fermentation and contributes to its climatic adaptation. This study aimed to characterize the rumen microbiota responses to wide seasonal variations, especially those necessary for survival in the cold seasons. Methods and Results In the present study, we performed 16s rRNA gene sequencing to investigate the seasonal variations in microbiota composition, diversity, and associated volatile fatty acids (VFAs) in yak rumen. The results showed that rumen microbiota were dominated by Bacteroides (72.13%–78.54%) and Firmicutes; the relative abundance of Firmicutes was higher in summer (17.44%) than in winter (10.67%; P < 0.05). The distribution of taxa differed among spring, summer, and winter rumen communities (PERMANOVA, P = 0.001), while other taxa (e.g., Fibrobacter, Verrucomicrobia, Anaerostipes, and Paludibacter) which could potentially help overcome harsh climate conditions were observed in higher abundance during the cold spring and winter seasons. The highest total VFA concentration in the yak rumen was obtained in summer (P < 0.05), followed by spring and winter, and both positive and negative correlations between VFAs and specific genera were revealed. Conclusions Microbiota in yak rumen appear to be highly responsive to seasonal variations. Considering environmental factors, we suggest that seasonal adaptation by microbial communities in rumen enables their hosts to survive seasonal scarcity and cold stress in the spring and winter. Significance and Impact of Study The present study furthers our understanding of how microbial adaptation to seasonal variations in nutrient availability and climate may function in high plateau ruminants, providing insights into the tripartite relationship between the environment, host, and microbiota.

Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3′-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.

Although coat color is an important economic phenotype in domesticated yaks (Bos grunniens), its genetic basis is not yet fully understood. In this study, a genome-wide selective sweep and high-frequency runs of homozygosity (ROH) identification were performed on 50 yaks with different coat colors to investigate candidate genes (CDGs) related to coat color. The results suggested that 2263 CDGs were identified from the 5% interaction windows of the F_ST and θπ ratio, along with 2801 and 2834 CDGs from black and brown yaks with iHS, respectively. Furthermore, 648 and 691 CDGs from black and brown yaks, which were widely enriched in pathways related to melanogenesis, melanocyte differentiation, and melanosome organization via GO and KEGG functional enrichment, respectively, were confirmed on the basis of the intersection of three parameters. Additionally, the genome of brown yaks presented more ROH, longer ROH fragments, and higher inbreeding levels than those of black yaks. Specifically, a large number of genes related to melanin synthesis and regulation (e.g., UST, TCF25, and AHRR) from the ROH islands were confirmed to be under strong selection. In summary, the results of this study enhance the understanding of the genetic basis for determining yak coat color.

Background: Yak as a unique domestic animal that has extremely important social value and influence on the local culture and economy in the Qinghai-Tibet Plateau. The current study aimed to evaluate the genotype distribution of a series of economic traits (growth, meat quality and lactation) related to single nucleotide polymorphisms (SNP) in three Tibetan yak populations. Methods: A total of 238 yaks from three populations [Sibu (SB), Chawula (CWL) and Jiali (JL) yaks] including 34 SB, 104 JL and 100 CWL yak individuals were collected. All samples were genotyped for 12 SNP markers by using SNaPshot technology. Result: All loci had abundant polymorphisms in the three populations, except for the Hesx1_G618C locus. The dominant growth-related genotype was MyoD1_C1710T (C/T), which had the highest frequency in the three Tibetan yak populations. However, the growth-related dominant genotypes at UCP2_T1499C (C/T) and CYP4A11_G4806A (G/A) loci were rare genotypes in the three Tibetan yak populations. Results of Hardy-Weinberg equilibrium (HWE) analysis showed that all sites did not deviate from the HWE within the population. This finding indicated that these populations belonged to a natural one without having been subjected to artificial selection on economic traits. Overall, this study provided valuable reference for the future molecular breeding of yak based on the genotype distribution of economic-trait candidate markers in three yak populations in Tibet.

Diet composition is a crucial yet understudied, dimension of animal ecology, with seasonal dietary shifts being a key factor in the population dynamics of large herbivores. However, characterizing these variations and their drivers in free‐ranging animals has been challenging due to their high mobility and the diverse plant species in their diet. According to optimal foraging theory, animals select their diet to maximize energy intake, a decision process that involves evaluating the abundance and quality of potential food sources. We determined the seasonal dietary shifts and food network in high‐altitude grazing yaks using DNA metabarcoding targeting the trn L region of fecal samples. Seasonal shifts in yak diet composition were structured by resource heterogeneity and influenced by plant community diversity and aboveground biomass. Dietary diversity and richness were greater in winter than summer, while plant community diversity and species richness exhibited opposite trends. This pattern indicated that yaks exhibited the strongest dietary selection during the summer with high resource abundance. Less selection in winter led to more diet dissimilarities, possibly reflecting a compensatory strategy to mitigate energetic deficits by broadening dietary niche breadth and maximizing resource availability under food limitation conditions. The proportion of forbs consumed by yaks was highest in both summer and winter, while the intake of sedges and grasses increased significantly in winter, suggesting that yaks selected high‐protein forbs over grasses or sedges. Our results support the predictions from optimal foraging theory, demonstrating that the energetic basis of dietary selection governs niche width in seasonal environments. Consistent with predictions from optimal foraging theory, our study shows that the energetic drivers of diet selection determine niche breadth in seasonal environments.