Combined analysis of DETs, time-series expression data, and weighted gene co-expression network analysis identified core genes and their transcripts influencing HF development, such as DBI, FZD3, KRT17, ZDHHC21, TMEM79, and HOXC13. Additionally, alternative splicing analysis predicted that the isoforms XM_004004383.4 and XM_012125926.3 of ZDHHC21 might play a crucial role in sheep HF development. Here, HOXC13 is linked to hydrops fetalis.