Diarrhea is associated with gut microbiota, immunity, and metabolic alterations in goat kids and lambs. This study used 28 lambs (11 healthy and 17 diarrheic) and 20 goat kids (10 healthy and 10 diarrheic) to investigate the association between diarrhea occurrence and changes in gut microbiota, metabolism, and immunity in goat kids and lambs. The results revealed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla in goat kids and lambs. In addition, Enterobacteriaceae and Lachnospiraceae families were identified in both diarrheic goat kids and lambs. Furthermore, functional prediction of microbiota showed that it was involved in cell motility and cancer pathways. The identified differential metabolites were implicated in the bile secretion pathway. Lambs had significant differences in immunoglobulin G (IgG), immunoglobulin M (IgM), interleukin-1β (IL-1β), and tumor necrosis factor-alpha (TNF-α) compared to goat kids. IgG and IL-1β were positively correlated to Patescibacteria, Clostridiaceae, and unclassified_Muribaculaceae in both diarrheic goat kids and lambs. In addition, weighted gene co-expression network analysis (WGCNA) revealed that the MEgreen module was positively associated with IgG, IgM, IL-1β, TNF-α, and triglyceride (TG). In conclusion, our results characterized the gut microbiota, metabolism, and immune status of lambs and goat kids suffering from diarrhea.

Hexi cattle are a local cattle population endemic to the Hexi Corridor in Gansu Province, China, and exhibit strong adaptability to the region’s arid continental environment. However, comprehensive genomic investigations of this population are still lacking. In the present study, we integrated population genomic analyses with a genome-wide association study (GWAS) to dissect the genetic architecture of Hexi cattle. Whole-genome resequencing data were generated for 264 Hexi cattle, and public genomic datasets from six representative cattle breeds were obtained from the NCBI database for comparative analysis. Multiple analytical approaches—including principal component analysis (PCA), linkage disequilibrium (LD) decay analysis, neighbor-joining (NJ) phylogenetic tree construction, and ADMIXTURE analysis—were adopted to evaluate population structure and evolutionary relationships. A mixed linear model was then used to identify significant SNPs associated with five major body conformation traits in six-month-old cattle: body weight (BW), withers height (WH), hip height (HH), heart girth (HG), and abdominal girth (AG). Our results confirm the admixed nature of Hexi cattle, whose genome is derived primarily from Simmental cattle and secondarily from Mongolian cattle. A total of 69 trait-associated significant SNPs were identified and functionally annotated. Specifically, TBC1D31, DERL1 and MCPH1 were linked to BW; FSCN3 and PLBD1 to WH; MCPH1 to HH; NPAS3, TBC1D31, DERL1 and MCPH1 to HG; and SOX5, NTAQ1, FAM83A, TBC1D31, DERL1, CDH11, CPLX4 and ADAM18 to AG. This study deepens our understanding of the genetic basis of growth traits in Hexi cattle and offers valuable molecular resources for future selective breeding, genetic improvement, and long-term conservation of this indigenous cattle population.

Hexi cattle are an indigenous beef population developed through multigenerational crossing of Simmental and Mongolian cattle, exhibiting exceptional adaptability to arid and semi-arid environments alongside robust growth performance. To investigate the genetic architecture underlying early growth traits, we conducted a GWAS for body weight (BW), withers height (WH), body length (BL), and heart girth (HG) in a cohort of 264 Hexi cattle (125 males, 139 females). Phenotypic analyses showed that male calves had significantly higher values for all traits relative to female calves (p < 0.05), confirming the presence of sexual dimorphism. The genomic inflation factors (λ = 0.997–1.016) indicated that population structure was effectively controlled. In total, 11 functional candidate genes were identified under the genome-wide significant threshold of p < 1.0 × 10⁻⁶. Specifically, SLC44A1 associated with BW; PTGS2, POP1, and ERC2 with WH; TIAM1, PROK1, SMOC2, and RFFL with BL; and C3orf80, PROKR1, and FBXO32 with HG. These results not only advance our understanding of the genetic regulation of early development in Hexi cattle but also establish a foundation for implementing marker-assisted and genomic selection in this population.