Abstract
The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) and histological observations were performed using the Holstein dairy cow mammary gland to explore gene expression patterns in this process of decrease (at peak, mid-, and late lactation). Histological observations suggested that the number of mammary acinous cells at peak/mid-lactation was significantly higher than that at mid-/late lactation, and the lipid droplets area secreted by dairy cows was almost unaltered across the three stages of lactation (p > 0.05). Totals of 882 and 1439 genes were differentially expressed at mid- and late lactation, respectively, compared to peak lactation. Function analysis showed that differentially expressed genes (DEGs) were mainly related to apoptosis and energy metabolism (fold change ≥ 2 or fold change ≤ 0.5, p-value ≤ 0.05). Transcriptome analysis based on STEM identified 16 profiles of differential gene expression patterns, including 5 significant profiles (false discovery rate, FDR ≤ 0.05). Function analysis revealed DEGs involved in milk fat synthesis were downregulated in Profile 0 and DEGs in Profile 12 associated with protein synthesis. These findings provide a foundation for future studies on the molecular mechanisms underlying mammary gland development in dairy cows.
Highlights
Milk is a traditional food source with balanced nutrition, and it has constituted an important part of the human diet since ancient times [1]
R based on the hypergeometric distribution was determined to identify significant gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways compared with the entire genomic background [31], setting a false discovery rate (FDR) ≤ 0.05 as a threshold
The formula for calculation was as follows (1), in which M denotes the number of genes annotated in a pathway and m denotes the number of differentially expressed genes (DEGs) in M; N denotes the number of genes annotated in a pathway, and n denotes the number of DEGs in N
Summary
Milk is a traditional food source with balanced nutrition, and it has constituted an important part of the human diet since ancient times [1]. Exploring the gene expression levels of the bovine mammary gland is helpful in revealing the biological mechanism of mammary morphogenesis, metabolic activity, and milk composition synthesis [9]. Transcriptome sequencing has been used to analyze the transcripts of the mammary gland of Holstein dairy cows at different periods of lactation. To explore the gene expression profile alterations during non-lactation (early stage of pregnancy) versus mid-lactation, transcriptomic analysis was used to identify differentially expressed genes (DEGs) in the mammary gland of Holstein dairy cows [7]. To reveal the expression changes of key mammary gland genes related to lactation decline in dairy cows, we, for the first time, determined the expression variations in mammary gland genes of Holstein dairy cow during peak, mid-, and late lactation, and we analyzed the data using the short time-series expression miner (STEM) clustering method. Our findings will help to clarify the mechanism of milk production and will have potential application value for improving the quality of dairy products
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