Sustainability & efficiency

Genomic scans for dry matter intake, consistency of dry matter intake, and residual feed intake in lactating dairy cows using imputed whole-genome sequence data

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Abstract

Feed is the most important operational cost in dairy farming. Genetic selection for feed efficiency is an important tool to improve production efficiency while reducing the environmental impact of dairy production. The identification of genetic variants and individual genes affecting feed efficiency could have multiple benefits, including better understanding the genetic basis of this complex phenotype, as well as obtaining more accurate genomic predictions. Thus, the aim of this study was to use imputed whole-genome sequence data to identify genetic variants and individual genes affecting dry matter intake (DMI), consistency of DMI, calculated as the logarithmic variation of DMI, and residual feed intake (RFI) in mid-lactation cows. Data consisted of 7,623 Holstein cows enrolled in 142 trials in eight research stations across the United States between 2007 and 2025. For each cow, only records between 50 and 200 days in milk were considered for the analysis. All cows had genotypic information for 69k SNP markers. Two consecutive rounds of imputation were performed: first, the 7,623 cows were imputed from 69k to 309k SNP markers. This imputation was performed using a reference set of 7,427 proven Holstein bulls with 309k SNP markers. Then, the 7,623 cows were imputed from 309k markers to whole-genome sequence data. This second round of imputation used 180 US Holstein bulls from the 1000 Bulls Genome Project as a reference set. Only autosomal markers with minor allele frequency larger than 1% were retained for the genomic scans. After quality control, 12.9 M markers were available for analysis. The three traits were analyzed using a two-step mixed model-based approach. For that analysis, a genomic relationship matrix was created using 69,999 SNPs randomly selected proportionally to the size of each chromosome. In the first step, the fitted models included the random effect of cow, and the fixed effects of cohort, days in milk, and lactation for DMI and consistency of DMI. In the second step, genomic scans were used to estimate single SNP effects. The mean (± SD) values for DMI, RFI, and consistency of DMI were equal to 24.83 ± 3.89 kg, 0.00 ± 1.63 kg, and 1.77 ± 0.69, respectively. The heritability estimates based on genomic information were 0.33 for DMI, 0.19 for RFI, and 0.25 for consistency of DMI. Quantile-quantile (Q-Q) plots showed that the test statistics appeared well behaved, with little evidence of significant associations. Similarly, the Manhattan plots did not show regions with major peaks. These findings suggest that DMI, RFI, and consistency of DMI are highly polygenic traits, influenced by many genes with small individual effects. Future work includes uncovering biological pathways and molecular mechanisms that influence these traits using enrichment tools.

Keywords: 2026

How to Cite:

Kirkpatrick, B., Koltes, J., Nascimento, B., Parker Gaddis, K., Peà±agaricano, F., Santos, J., Tempelman, R., VandeHaar, M., Weigel, K. & White, H., (2026) “Genomic scans for dry matter intake, consistency of dry matter intake, and residual feed intake in lactating dairy cows using imputed whole-genome sequence data”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2274169. doi: https://doi.org/10.31274/wcgalp.23420

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