Long Intergenic Non-Coding RNAs in the Mammary Parenchyma and Fat Pad of Pre-Weaning Heifer Calves: Identification and Functional Analysis

SIMPLE SUMMARY: The development of mammary gland is directly related to the productivity of dairy animals. Some studies showed that feeding the enhanced plane of nutrition at pre-weaning stage are advantageous to the development of mammary gland. However, regulators which are involved in this biological process remain largely unknown. In this work, we have identified some long intergenic non-coding RNAs (lincRNAs) in mammary parenchyma (PAR) and mammary fat pad (MFP) of heifer calves under different levels of nutrition at pre-weaning stage by using the published RNA-seq database. Furthermore, those putative lincRNAs, which were highly correlated with these key protein-coding genes in mammary gland development, were highlighted. Our results not only confirmed the advantages of feeding calves with enhanced feeding plane in pre-weaning stage, but also provided fundamental base for further research on the biological processes of mammary gland development. ABSTRACT: Enhanced plane of nutrition at pre-weaning stage can promote the development of mammary gland especially heifer calves. Although several genes are involved in this process, long intergenic non-coding RNAs (lincRNAs) are regarded as key regulators in the regulated network and are still largely unknown. We identified and characterized 534 putative lincRNAs based on the published RNA-seq data, including heifer calves in two groups: fed enhanced milk replacer (EH, 1.13 kg/day, including 28% crude protein, 25% fat) group and fed restricted milk replacer (R, 0.45 kg/day, including 20% crude protein, 20% fat) group. Sub-samples from the mammary parenchyma (PAR) and mammary fat pad (MFP) were harvested from heifer calves. According to the information of these lincRNAs’ quantitative trait loci (QTLs), the neighboring and co-expression genes were used to predict their function. By comparing EH vs R, 79 lincRNAs (61 upregulated, 18 downregulated) and 86 lincRNAs (54 upregulated, 32 downregulated) were differentially expressed in MFP and PAR, respectively. In MFP, some differentially expressed lincRNAs (DELs) are involved in lipid metabolism pathways, while, in PAR, among of DELs are involved in cell proliferation pathways. Taken together, this study explored the potential regulatory mechanism of lincRNAs in the mammary gland development of calves under different planes of nutrition.