Correlation of Coding and Non-Coding RNAs on the Fat Deposition of Yaks Under Different Feeding Systems

The yak is a classic grazing livestock species on the Qinghai-Tibet Plateau, and fat deposition is indispensable for its survival and metabolism. Coding and non-coding RNAs (ncRNAs) play an important role in regulating fat deposition in livestock. In this study, the expression of mRNAs, lncRNAs, miRNAs, and circRNAs in the subcutaneous fat of yaks under grazing and stall feeding was measured using whole-transcriptome sequencing technology. A total of 677 differentially expressed (DE) mRNAs, 120 DE lncRNAs, 2216 DE circRNAs, and 15 DE miRNAs were identified, and their biological function was explored using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Co-expression RNA (ceRNA) networks between DE ncRNAs and DE mRNAs were further constructed, and the crucial RNAs and signal pathways regulating fat deposition in yaks were obtained. The effect of mRNAs and ncRNAs on fat deposition in yaks mainly depended on the PPAR, PI3K-Akt, and cAMP signaling pathways, and the regulatory pathways TCONS00042948, TCONS00012083/bta-miR-2316/MCAT, and NR4A3 may be critical in this process. This study provides some theoretical basis for breeding yak species and promotes improvements in yak production.