GWAS & Selection signatures

Runs of Heterozygosity and their Association with Productive Traits in Mexican Holstein Cattle

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Abstract

Runs of heterozygosity (ROHet) have been used to identify genomic regions that are under gene introgression or admixture. Additionally, avoid the deleterious effects of harmful homozygous genotype aggregation on specific traits and maintain heterozygote advantages in many characteristics of productive, reproductive and health interest. The objective of this study was to characterize ROHet in the Mexican Holstein population and to assess their association with milk, fat, and protein yield. A total of 12,162 genotyped animals with different SNPs arrays (6, 11, 14, 26, 33, 35, 40, 60, 65, 91, 115, y 116 K) and previously imputed to 116,204 SNPs were analyzed. The dataset resulted from an imputation and quality control process in which markers and individuals with a call rate below 0.9 were excluded, along with SNPs showing a minor allele frequency below 0.015 and a Hardy-Weinberg equilibrium p-value lower than 0.0001. ROHet were identified using the consecutive SNP run detection approach implemented in the detectRUNS package of R version 4.5.1. Detection parameters were set to a minimum of 15 consecutive SNPs per run, a minimum length of 10,000 kb, a maximum allowed gap between SNPs of 500,000 kb, no homozygous SNPs were permitted, and a maximum of one missing SNP per segment. In total, 6,839 repeated ROHet (shared among multiple animals) and 237,439 unique ROHet (present in only one animal) were detected. The majority of ROHet were shorter than 0.5 Mb (82.59%), followed by those between 0.5 and 1 Mb (15.11%) and 1-2 Mb (2.17%), while segments exceeding 2 Mb were rare (0.013%). For the association analysis, only ROHet present in at least 10% of the population were retained, yielding 38 ROHet. Associations with productive traits were evaluated using the BLUPF90+ program through a linear model that included month of calving, herd-year, and age at calving as fixed effects; the 38 ROHet as covariates; and animal as a random effect. The significance of each ROHet was tested through the regression coefficient (β) using a t-test. Among the analyzed segments, 36 ROHet were significantly associated with milk yield, 35 with fat yield, and 33 with protein yield. These findings indicate that specific genomic regions displaying heterozygosity may contribute to enhanced milk productivity in Holstein cattle. The results suggest that ROHet are key candidates for selection programs, where maintaining heterozygosity at specific loci could be an effective strategy to improve productive performance and counteract the negative effects of inbreeding.

Keywords: 2026

How to Cite:

Trejo-Díaz, L., García-Ruiz, A., Toledo-Alvarado, H. & Ruiz-López, F., (2026) “Runs of Heterozygosity and their Association with Productive Traits in Mexican Holstein Cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286807. doi: https://doi.org/10.31274/wcgalp.24127

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