Identification of long non-coding RNAs in the early growth stage of Holstein mammary gland

In Holsteins, emerging evidence suggests that long non-coding RNAs (lncRNAs) are actively involved in the regulation of mammary gland development. However, the lncRNA expression pattern in the early growth stage of Holstein mammary gland remains little known. In this study, we comprehensively analyzed 11 mammary gland tissue RNA-Seq datasets derived from Holstein heifer calves (ca. 8 weeks old) retrieved from the Sequence Read Archive database. We identified a total of 588 lncRNAs in the intergenic region. By comparing the sequences with NONCODEv5 database, 241 novel lncRNAs were detected in the mammary gland. Prediction of <i>cis</i>-regulated target gene revealed that 364 out of 588 lncRNAs potentially targeted 417 protein-coding genes. Furthermore, Gene Ontology enrichment determined that potential target genes were mainly involved in the terms associated with energy metabolism and cell differentiation, such as cellular respiration, respiratory electron transport chain, electron transport chain, and regulation of cell differentiation, which were closely related to mammary gland development. This study provides potential candidate lncRNAs in regulating mammary gland development in the early growth stage of Holsteins, as well as a better general understanding of Holstein mammary gland development.