Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle.

Chinese red steppe cattle, a highly developed breed for their meat and milk, are not well known about the formation mechanisms for high-quality beef. Furthermore, many fundamental investigations of cattle are hampered by deficient full-length cDNAs. Here, we utilized ONT full-length transcript sequencing from 9 bovine preadipocytes during 3 periods to find 2502 novel genes and 3253 novel transcriptomes, further improving the quality of reference genome annotation. At the same time, based on diverse expression patterns in 3 periods (early, middle and late), we identified 754 significantly differentially expressed genes (DEGs) and 932 significantly differentially expressed transcripts (DETs) in the first contrast group (0d_vs_4d), 197 significantly DEGs and 297 significantly DETs in the second contrast group (0d_vs_8d), 465 and 555 significantly DEGs and DETs in the third contrast group (4d_vs_8d). These DEGs mainly enriched the pathways related to cell differentiation such as Wnt signaling pathway and positive regulation of fat cell differentiation. A total of 35,616 alternative splicing (AS) events were detected, in which 111, 109 and 101 significantly different AS events were found in the group 0d_vs_4d, 0d_vs_8d and 4d_vs_8d respectively. In particular, two essential DEGs, N4BP2L1 and PRKAA1 related to cell differentiation were shown to take part in distinct AS events and were therefore considered as key candidate genes for improving fat deposition and meat quality in Chinese red steppe cattle. These findings provide novel insights into the adipocyte differentiation in cattle and metabolic processes that regulate fat storage, which is essential for optimizing growth and production.