Diet Composition Affects Liver and Mammary Tissue Transcriptome in Primiparous Holstein Dairy Cows

Abstract

The objective of the present study was to evaluate the overall adaptations of liver and mammary tissue to a corn stover (CS) compared to a mixed forage (MF) diet in mid-lactation primiparous dairy cows. Twenty-four primiparous lactating Holstein cows were randomly allocated to 2 groups receiving either an alfalfa forage diet (MF, F:C = 60:40) with Chinese wildrye, alfalfa hay and corn silage as forage source or a corn stover forage diet (CS, F:C = 40:60). A subgroup of cows (n = 5/diet) was used for analysis of liver and mammary transcriptome using a 4 × 44K Bovine Agilent microarray chip. The results of functional annotation analysis showed that in liver CS vs. MF inhibited pathways related to lipid metabolism while induced the activity of the potassium channel. In mammary tissue, fatty acid metabolism was activated in CS vs. MF. In conclusion, the analysis of genes affected by CS vs. MF indicated mammary gland responding to lower level of linoleate from the diet (lower in CS vs. MF) by activating the associated biosynthesis metabolic pathway while the liver adaptively activated potassium transport to compensate for a lower K ingestion.

Keywords: corn stover; forage-to-concentrate ratio; liver and mammary gland; transcriptome.

Figure 1

Volcano plot for the genes statistically (A false discovery rate (FDR) < 0.2) affected by corn stover (CS) vs. mixed forage (MF) diet in both liver and mammary tissue (CS/MF; 140 up- and 152 down-regulated), liver (CS/MF Liver; 56 down- and 83 up-regulated), and mammary tissue (CS/MF Mammary; 63 up-D and 57 down-regulated). Red and blue dots represent upregulated and downregulated DEG, respectively.

Figure 2

Summary of the main categories and sub-categories of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways as results of the transcriptomic effect on mammary (M) and liver (L) tissue of corn stover (CS) compared to mixed forage (MF) ration in dairy cows as analyzed by the Dynamic Impact Approach. On the right are the bar denoting the overall impact (in blue) and the shade denoting the effect on the pathway (from green—inhibited—to red—activated). Darker the color larger the activation (if red) or inhibition (if green) of the pathway.

Figure 3

The 10 most impacted pathways in liver (CS/MF Liver), mammary (CS/MF Mammary), and overall of liver and mammary (CS/MF) of corn stover (CS) compared to mixed forage (MF) ration in dairy cows uncovered by the Dynamic Impact Approach. On the right are the bar denoting the overall impact (in blue) and the shade denoting the effect on the pathway (from green—inhibited—to red—activated). Darker the color larger the activation (if red) or inhibition (if green) of the pathway.

Figure 4

Functional analysis results revealed by Database for Annotation, Visualization, and Integrated Discovery (DAVID) analysis of the transcripts up- (in red shade in the figure) or down- (in blue shade in the figure) regulated by corn stover (CS) compared to mixed forage (MF) in both liver and mammary (CS/MF), in liver tissue alone (CS/MF Liver), or mammary tissue alone (CS/MF Mammary). GO_MF: Gene Ontology Molecular Function; GO_CC: Gene Ontology Cellular Component; GO_BP: Gene Ontology Biological Process; KEGG: Kyoto Encyclopedia of Genes and Genomes.

Figure 5

Functional annotation for liver and mammary in CS (corn stover) compared to MF (mixed forage) uncovered by ClueGO. Shown are the enriched terms in DEG between CS vs. MF. Particularly: (A) down-regulated DEG in liver; (B) up-regulated DEG in liver; C: down-regulated DEG in mammary tissue; (D) up-regulated DEG in mammary tissue. The size of the nodes reflects the statistical significance of each term. Larger the node size, smaller the P-value. The name of each group is given by the most significant term/pathway of the group. The nodes are grouped by similarity of their associated genes. The nodes in hexagon represents the terms of GO Cellular Component; the nodes in octagon represents the terms of GO Molecular Function; the nodes in rectangle represents the KEGG pathway. The small circles with symbols in red font represent the genes associated with the corresponding terms or pathways.