Omics & gene networks

Transcriptomic profiling of high and low feed efficiency in lactating Holstein dairy cows from whole blood

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Abstract

Feed efficiency impacts the economic viability and environmental sustainability of dairy production, making it a critical trait to improve. Feed efficiency in this study was defined as residual feed intake (RFI), which is the difference between an animal's actual and predicted feed intake after accounting for production and maintenance energy requirements. Unfortunately, little is known about the genetics of RFI. The objective of this study was to identify genes involved in RFI performance using whole blood sampling as a minimally invasive way to identify differentially expressed genes (DEGs). Cows within the top and bottom 15 percentiles for RFI within a population of 329 lactating Holstein cows had whole blood samples collected for RNA-sequencing (RNA-seq) using QuantSeq chemistry to identify DEG. The final RNA-Seq dataset included 21 cows: 10 classified as high feed-efficient (desirable, low RFI) and 11 as low feed-efficient (undesirable, high RFI). Sequence reads were aligned to the Bovine ARS-UCD2.0 genome using Ensembl v115 annotations. The model fit in DESeq2 software to identify DEGs included RFI as a category (high or low), contemporary group, parity classified as 1, 2, or 3+, and days in milk classified as early, mid, peak, or late. A total of 226 genes were identified as DEG (adjusted p-value 2), of which 87 were increased and 139 were decreased in abundance in the high-efficiency group relative to the low-efficiency group. Of the DEGs, 79 genes were annotated as long non-coding RNAs (lncRNAs), comprising 57 decreased and 22 increased in abundance. This abundance of lncRNAs suggests the presence of an additional post-transcriptional regulatory layer that may influence metabolism and physiology in high versus low RFI cows. KEGG enrichment analysis of the DEGs identified 120 significantly enriched metabolic pathways (adjusted p-value UTP15 and RPL3L, both of which are involved in ribosomal biogenesis. Functional enrichment analysis revealed that this RFI-associated network was significantly enriched for biological processes related to ribosomal function, ribosomal biogenesis, and RNA degradation (adjusted p-value < 0.001). Given that ribosomal proteins also contribute to immune signaling, these findings suggest potential links between immune regulation and feed efficiency measured as RFI. These findings provide a systems-level perspective on how metabolic, signaling, and regulatory networks collectively may influence feed efficiency and immune function.

Keywords: 2026

How to Cite:

James, L., Mayes, M., Siberski-Cooper, C., Lim, K. & Koltes, J., (2026) “Transcriptomic profiling of high and low feed efficiency in lactating Holstein dairy cows from whole blood”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286647. doi: https://doi.org/10.31274/wcgalp.24078

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