Gene function & annotation

A Census of Chromosomal Error: SNP Data Reveal Viable Aneuploid Livestock

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Abstract

Aneuploidy, defined by the loss or gain of entire chromosomes, is a significant cause of infertility, developmental abnormalities, and reduced life expectancy in mammals. Aneuploidy has traditionally been detected by karyotyping infertile or malformed individuals; however, this approach obscures the true prevalence and phenotypic spectrum of aneuploidy. Access to single nucleotide polymorphism (SNP) genotypes now enables large-scale screening for aneuploidy.SNP 50K array data from 21,694 horses, 779,138 cattle, and 63,444 sheep classified as juveniles at the time of genotyping (≤1 year, ≤15 months, ≤8 months, respectively) were used to determine the population-level prevalence of aneuploidy. The B-allele frequency (BAF) and Log R Ratio (LRR) values were used to identify animals with autosomal and sex-chromosome (chr) aneuploidies (XO, XXX, XXY). Putative cases were confirmed via visual inspection of Manhattan plots of LRR and BAF values, with a subset further validated by karyotyping.Across species, the highest prevalence of monosomy X (XO) was observed in horses (0.145% of females), occurring at approximately 1.1 times the rate in sheep (0.126% of females) and over 36 times the rate in cattle (0.0048% of females). In contrast, trisomy X (XXX) was most prevalent in cattle (0.035% of females). The incidence of Klinefelter syndrome (XXY) was highest in horses (0.107% of males), a rate of 1.5 times that in sheep (0.071% of males) and 1.2 times that in cattle (0.087% of males). Autosomal trisomies were rare but present in all species, with a collective prevalence of approximately 0.017% in sheep, 0.017% in cattle, and 0.030% in horses. Sex-chromosome aneuploidies (XO, XXX, XXY) were generally associated with infertility, whereas the severity of each autosomal trisomy was highly variable and linked to autosome size and gene content. In cattle, trisomy of smaller autosomes (e.g. chr26, chr27, chr28, chr29) was observed in some animals that survived to adulthood, with some cases even being fertile (e.g. chr27, chr28), whereas trisomies of larger chromosomes (e.g chr12, chr15, chr20, chr24) were all lethal within 14 days of birth. A similar pattern was observed in sheep, where trisomy of larger chromosomes (chr6, chr16, chr18, chr23) resulted in perinatal mortality, while one trisomy case involving the smaller chr26 survived to 213 days. In horses, the sole autosomal trisomy detected was of the small, gene-poor chr27. The relative scarcity of autosomal trisomy in horses is likely attributable to the smaller dataset size and the practice of genotyping at later ages, which precludes detection of early lethal cases.This multi-species study revealed that many chromosomal abnormalities, including fertile cases, are more common in livestock than previously thought. For breed societies and registries already genotyping, adding low-cost chromosomal screening at registration could identify affected animals early and avoid the downstream costs of undiagnosed infertility and related issues.

Keywords: 2026

How to Cite:

Ryan, C., Doyle, J., McHugh, N. & Berry, D., (2026) “A Census of Chromosomal Error: SNP Data Reveal Viable Aneuploid Livestock”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286168. doi: https://doi.org/10.31274/wcgalp.23866

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