Integrated transcriptome and microbiome analysis reveals lactation performance between Sewa sheep and East Friesian sheep

Lactation performance is a critical economic trait in sheep production. The Sewa sheep (SWS), a native dual-purpose meat and dairy breed unique to the Qinghai-Tibet Plateau, exhibits significantly lower milk yield, while the East Friesian sheep (EFS) is renowned as one of the world's highest-performing dairy sheep breeds. However, the role of host gene expression factors in regulating rumen microbial community-mediated lactation processes in sheep remains unclear. Histological examination shown that SWS exhibited smaller mammary acini area, lipid droplet area, and lipid droplet diameter compared to EFS. Transcriptomic profiling of mammary gland tissues identified 1,163 differentially expressed genes (DEGs), with 269 up-regulated and 894 down-regulated. Function enrichment analysis indicated that these DEGs were involved in lactation-related pathways, including PI3K-Akt signaling, mTOR signaling, carbon metabolism, and oxidative phosphorylation. Furthermore, 16S rRNA sequencing of rumen fluid demonstrated significant differences in microbial community composition between the two breeds at both the phylum and genus levels. Integrated analysis identified CDC42,LAMA5 and NOTCH1 as key candidate genes associated with lactation regulation, along with Verrucomicrobiota, Selenomonas , Butyrivibrio , and Actinobacteria as potential microbial contributors to the lactation process. Collectively, these findings provide valuable guidelines for regulating lactation through genetic expression and microbial management strategies in sheep.