Conservation & local programs

Geographic characterization of Hereford cattle genetics in the United States

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Abstract

This study used geographic region to quantify changes in the genetic diversity of American Hereford Association (AHA) registered cows. Genetic diversity within a breed is dynamic and depends on environmental conditions and traits important to breeders, both exerting artificial and natural selection pressures on the breed. Hereford cattle are raised in all U.S. environmental regions and have a national genotyping program for the population. Genotypes from 3,426 Hereford cows born between 2011 and 2024 were obtained from AHA. All cattle were genotyped using the GeneSeek Genomic Profiler Bovine 100K panel. Quality control filtered single-nucleotide polymorphisms (SNPs) and individuals with more than 10% missingness, leaving 87,333 SNPs and 3,416 animals. The AHA regions were the basis for classifying animals into East, Midwest, North Central, Southwest, Mountain, and Western. Principal component, ADMIXTURE and pairwise fixation index (FST) analyses were used to quantify genetic diversity patterns. Top FST values were used to identify SNP associated with conception rate or milk production. The first four principal components explained 47.78% of the genetic variation. Across all SNP sets, the averaged principal components 1 and 2 revealed distinct clustering by region. Averages for Mountain, Western, and Southwest were separated by an x-axis origin line from North Central, Midwest, and East. ADMIXTURE runs indicated that the breed was partitioned into 4 clusters. The four clusters corresponded primarily to East, Midwest, North Central, and Mountain regions. The horned and polled Hereford populations that were distinct for 94 years were present when partitioned into 2 clusters. The pairwise FST across regions ranged from 0.002 to 0.011. The FST values are low because the analysis was conducted within a singular breed. Of the SNPs identified with highest FST, five and nine SNPs had known associations with conception rate and milk production, respectively. Regional differences were observed for all 14 SNPs. One of the conception rate SNPs and 6 of the milk production SNPs had regional groupings separating Midwest, East, and North Central from the Southwest, Western, and Mountain regions. Across analyses, patterns of differentiation by region highlight geographic structuring of genetic diversity within the Hereford breed, with implications for resilience, adaptability, and increased production.

Keywords: 2026

How to Cite:

Giannini, M., Speidel, S., Enns, M., Sanders, S., Bedwell, S. & Blackburn, H., (2026) “Geographic characterization of Hereford cattle genetics in the United States”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2284863. doi: https://doi.org/10.31274/wcgalp.23618

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