Sustainability & efficiency

Genome-wide association study reveals shared genetic architecture of feed efficiency between calves and first parity Holstein cows

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Abstract

Early selection for feed efficiency offers a promising strategy to accelerate genetic progress while improving the sustainability and profitability of dairy production systems. Here we explore the genetic architecture underlying feed efficiency in Holstein cattle by identifying genomic regions and candidate genes associated with this trait within and across different life stages. Feed efficiency was evaluated using weekly averages of residual metabolizable energy intake (RMEI) in calves during the first (RMEI1) and second months of age (RMEI2), and residual feed intake (RFI) in first lactation cows. All animals came from the same research herd, with data collected from 2016 until 2024. Both traits were calculated as the difference between observed and predicted intake, with predicted intake estimated by regressing intake on metabolic body weight and average daily gain for calves, and on metabolic body weight and energy-corrected milk for cows, while adjusting for birth year-season and trial participation. The dataset included 12,246 RFI and 2,424 RMEI records across the two calf periods, with 443 animals having records in both life stages, 349 as calves only, and 265 as cows only. The dataset comprised 3,322 pedigree genotyped animals for 39,947 SNPs after quality control. A single-step genome-wide association study was performed using the BLUPf90 suite of programs. Significance thresholds were determined using Bonferroni correction based on the number of independent segments at a 5% chromosome-wise level. Candidate genes were defined within ±50 kb of significant SNPs, and QTL annotation was performed using the R package GALLO. A total of 43, 45, and 51 significant SNPs were identified for RMEI1 (across 8 BTAs), RMEI2 (across 15 BTAs), and RFI (across 16 BTAs), respectively. Within ±50 kb of these SNPs, 48, 44, and 56 genes were located, with 32 shared between RMEI2 and RFI, and only one (UNC13C, BTA10) common to all three periods. Notably, a large region on BTA10 (51.67-58.07 Mb), harboring 13 genes, was shared between RMEI2 and RFI. Regarding QTLs, 66 were detected for RMEI1 and RMEI2, and 58 for RFI. Among those associated with RMEI1, 48 were linked to milk production traits and 8 to reproductive traits, whereas for RMEI2 and RFI, 26 were related to milk traits and 15 to meat and carcass characteristics. The stronger genomic overlap between RMEI2 and RFI likely reflects the physiological transition from pseudo-monogastric digestion in the first month to ruminant digestion in the second month, making calves at this stage metabolically more similar to first lactation cows. These findings reveal key genomic regions and candidate genes associated with feed efficiency from early life to adulthood, providing insights into the genetic architecture of this trait and supporting the potential of early-life indicators for genetic selection in dairy cattle.

Keywords: 2026

How to Cite:

Ambrozio Galindo, B., Baes, C., Hermisdorff, I., Jahnel, R., Miglior, F., Phillips, A. & Schenkel, F., (2026) “Genome-wide association study reveals shared genetic architecture of feed efficiency between calves and first parity Holstein cows”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285781. doi: https://doi.org/10.31274/wcgalp.23792

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