<scp>NOA1</scp> deficiency observed in a subset of Montbéliarde calves with bilateral anophthalmia

Anophthalmia, defined as the congenital absence of one or both eyes, represents the most severe form of microphthalmia, a spectrum of ocular malformations that can occur either in isolation or as part of a broader syndrome (Verma & FitzPatrick, 2007; Goyal et al., 2025). In humans, where microphthalmia/anophthalmia (M/A) has been extensively studied, both environmental and genetic factors contribute to its development, with pathogenic variants identified in over 90 genes (Goyal et al., 2025; Harding & Moosajee, 2019). By contrast, no locus has yet been linked to M/A in cattle, prompting the present investigation. Since 2019, 14 cases of M/A in Montbéliarde calves have been reported to the French National Observatory for Bovine Abnormalities (Figure 1a,b) in herds free from known teratogenic viruses (e.g., bovine viral diarrhea, Bluetongue, Schmallenberg). These calves were neither particularly inbred nor closely related to each other within four generations, except for two full siblings born 1 year apart, which led us to suspect that at least some cases could be recessive. Under this assumption, we genotyped all affected calves and their parents using the Illumina EuroGMD SNP array (Boichard et al., 2018) and performed homozygosity mapping with a control group consisting of 29 833 adult cows and 3207 artificial insemination bulls, as previously described (Boulling et al., 2025; Mesbah-Uddin et al., 2019). All these controls were registered in the herdbook and therefore considered unaffected, as M/A is a cause for rejection due to incompatibility with the breed standard. This analysis revealed a peak on chromosome 6, where a 25-marker haplotype was homozygous in four of 14 affected calves but only seven of 33 040 controls (Bonferroni-corrected p = 1.23 × 10−7; Figure 1c). Notably, this interval (Chr6:71 589 866–72 783 452 bp on the ARS-UCD1.2 genome assembly) encompasses a recessive mitochondropathy locus caused by a frameshift insertion in NOA1 (NC_037333.1: g.72359797_72359798insG; Besnard et al., 2024; OMIA:002874-9913; Nicholas et al., 2024). Genotypes from a custom probe on the same array (Besnard et al., 2024) showed that the four M/A calves homozygous for the haplotype were also homozygous for the mitochondropathy variant, whereas the seven controls homozygous for the haplotype were heterozygous, probably due to persistence of an ancestral, non-mutated version of the haplotype at low frequency in the population. Interestingly, previous analyses of hundreds of thousands of Montbéliarde cattle genotyped at ~2–3 months for genomic evaluation revealed a major depletion of homozygous mutant individuals that could only partially be explained by reduced fertility from at-risk matings between heterozygous parents (Besnard et al., 2024). Specifically, it was estimated that approximately two-thirds of live-born homozygous mutants were not genotyped by breeders. Our finding of four NOA1−/− animals exhibiting bilateral anophthalmia (n = 3) or both anophthalmia and tail agenesis (n = 1) suggests that organ malformation, prompting early euthanasia, may account for this unexplained depletion. Supporting this hypothesis, complete knockout of Noa1 in mice is embryonically lethal (Kolanczyk et al., 2011), highlighting the critical role of this gene in early development. Moreover, three nuclear genes encoding mitochondrial proteins, as is the case for NOA1, have been linked to human forms of M/A: HCCS (Wimplinger et al., 2006), COX7B (Indrieri et al., 2012), and NDUFB11 (van Rahden et al., 2015). In conclusion, these findings suggest that NOA1 insufficiency may be a predisposing factor for bilateral anophthalmia. More broadly, they highlight the importance of studying naturally occurring deleterious variants in large livestock populations. Such investigations provide valuable insights into poorly characterized genes by revealing the range of pathological features associated with their loss of function (e.g., Bourneuf et al., 2017; Grohs et al., 2022). Finally, further research is needed to elucidate the etiology of the remaining cases of M/A observed in Montbéliarde cattle and other breeds. C.G. investigation; visualization; writing—review and editing. A.C. conceptualization; formal analysis; investigation; data curation; visualization; supervision; funding acquisition; writing—original draft. The authors would like to express their gratitude to S. Minéry (Idele), M. Courdier (Eva Jura), H. Tisserand (Genia'test), A. Rimbault (Montbéliarde Association), and the breeders and their veterinarians for providing information, samples, and photos. The authors declare no conflicts of interest. This work was supported by the Welcow project funded by APIS-GENE. All data supporting the findings of this study are provided in the present article or accessible through the cited references.