Long noncoding RNA (lncRNA) play a critical role in mammary development and breast cancer biology. Despite their important role in the mammary gland, little is known of the roles of lncRNA in bovine lactation, particularly regarding the molecular processes underlying it. To characterize the role of lncRNA in bovine lactation, 4 samples of Holstein cow mammary gland tissue at peak and late lactation stages were examined after biopsy. We then profiled the transcriptome of the mammary gland using RNA sequencing technology. Further, functional lncRNA-mRNA coexpression pairs were constructed to infer the function of lncRNA using a generalized linear model, followed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. More than 1,000 putative lncRNA were identified, 117 of which were differentially expressed between peak and late lactation stages. Bovine lncRNA were shorter, with fewer exon numbers, and expressed at significantly lower levels than protein-coding genes. Seventy-two differentially expressed (DE) lncRNA were coexpressed with 340 different protein-coding genes. The KEGG pathway analysis showed that target mRNA for DE lncRNA were mainly related to lipid and glucose metabolism, including the peroxisome proliferator-activated receptors and 5′ adenosine monophosphate-activated protein kinase signaling pathways. Further bioinformatics and integrative analyses revealed that 12 DE lncRNA potentially played important roles in bovine lactation. Our findings provide a valuable resource for future bovine transcriptome studies, facilitate the understanding of bovine lactation biology, and offer functional information for cattle lactation.

长非编码RNA（lncRNA）在乳腺发育和乳腺癌生物学中起着至关重要的作用。尽管它们在乳腺中起重要作用，但人们对lncRNA在牛泌乳中的作用知之甚少，特别是关于其基础的分子过程。为了表征lncRNA在牛泌乳中的作用，在活检后检查了4个处于高峰和哺乳后期的荷斯坦奶牛乳腺组织样品。然后，我们使用RNA测序技术分析了乳腺的转录组。此外，使用广义线性模型构建功能性lncRNA-mRNA共表达对，以推断lncRNA的功能，然后进行基因本体论和《京都议定书》中的基因与基因组百科全书（KEGG）途径分析。鉴定出了1,000多种推定的lncRNA，在高峰期和晚期哺乳期之间有117个差异表达。牛lncRNA较短，外显子数量较少，并且其表达水平明显低于蛋白质编码基因。72个差异表达（DE）lncRNA与340个不同的蛋白质编码基因共表达。KEGG通路分析表明DE lncRNA的靶mRNA主要与脂质和葡萄糖代谢有关，包括过氧化物酶体增殖物激活受体和5'腺苷单磷酸激活蛋白激酶信号通路。进一步的生物信息学和综合分析表明，12 DE lncRNA可能在牛泌乳中发挥重要作用。我们的发现为将来的牛转录组研究提供了宝贵的资源，有助于对牛泌乳生物学的理解，