Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process

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.

Analysis of reproduction-related transcriptomes on pineal-hypothalamic-pituitary-ovarian tissues during estrus and anestrus in Tan sheep

“…Pizzi et al ( 36 ) suggested that genes with similar expression have similar biological functions and work in concert. Fan et al ( 37 ) used STEM to examine genes associated with mammary development at peak, mid and late lactation in dairy cows and found that DEGs are mainly involved in apoptosis and energy metabolism, suggesting the reliability of the STEM analysis method. In the present study, we obtained four colored Clusters with the same trend (25, 24, 8, and 35) by STEM analysis of DEGs cross PHPO axis in Tan sheep.…”

Identification and Characterization of Circular RNAs Involved in the Flower Development and Senescence of Rhododendron delavayi Franch

“…The read counts of the circRNAs were converted into FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions of base pairs sequenced). Next, the STEM clustering method was utilized to analyze the expression trend of circRNAs from the budding to the fading of Rhododendron delavayi Franch [ 48 , 49 ]. For the STEM analysis, default parameters were used.…”

Transcriptome profiling of the nonlactating mammary glands of dairy goats reveals the molecular genetic mechanism of mammary cell remodeling

“…Transcriptome sequencing provides a high-throughput method for studying the molecular mechanisms of mammary gland development. Currently, a large number of studies have been carried out on transcriptome analysis of mammary gland or milk, involving goats (Crisà et al, 2016;Shi et al, 2016;Li et al, 2020), sheep (Paten et al, 2015;Wang et al, 2020), cattle (Bionaz et al, 2012;Zheng et al, 2018;Bhat et al, 2019;Fan et al, 2021), and pig (Shu et al, 2012;Palombo et al, 2018) at different stages of mammary gland development. Researches on the expression profile of mammary gland tissue after cessation of milking provide important clues to the molecules that may mediate epithelial cell death and tissue remodeling during involution (Clarkson et al, 2004;Stein et al, 2004;Shi et al, 2016).…”