An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle

Abstract

Researching depletions in homozygous genotypes for specific haplotypes among the large cohorts of animals genotyped for genomic selection is a very efficient strategy to map recessive lethal mutations. In this study, by analyzing real or imputed Illumina BovineSNP50 (Illumina Inc., San Diego, CA) genotypes from more than 250,000 Holstein animals, we identified a new locus called HH6 showing significant negative effects on conception rate and nonreturn rate at 56 d in at-risk versus control mating. We fine-mapped this locus in a 1.1-Mb interval and analyzed genome sequence data from 12 carrier and 284 noncarrier Holstein bulls. We report the identification of a strong candidate mutation in the gene encoding SDE2 telomere maintenance homolog (SDE2), a protein essential for genomic stability in eukaryotes. This A-to-G transition changes the initiator ATG (methionine) codon to ACG because the gene is transcribed on the reverse strand. Using RNA sequencing and quantitative reverse-transcription PCR, we demonstrated that this mutation does not significantly affect SDE2 splicing and expression level in heterozygous carriers compared with control animals. Initiation of translation at the closest in-frame methionine codon would truncate the SDE2 precursor by 83 amino acids, including the cleavage site necessary for its activation. Finally, no homozygote for the G allele was observed in a large population of nearly 29,000 individuals genotyped for the mutation. The low frequency (1.3%) of the derived allele in the French population and the availability of a diagnostic test on the Illumina EuroG10K SNP chip routinely used for genomic evaluation will enable rapid and efficient selection against this deleterious mutation.

A missense mutation (p.Tyr452Cys) in the CAD gene compromises reproductive success in French Normande cattle

“…Similarly, previous studies showed that haplotypes are not a perfect proxy for causal mutations (Michot et al, 2017;Fritz et al, 2018), and there are instances where 2 different versions of the same haplotype segregate in the population, one with and one without the causal mutation (Kipp et al, 2016;Menzi et al, 2016). Yet, haplotype is a good substitute to avoid carrier-tocarrier mating, when the causal mutation is unknown (VanRaden et al, 2011;Sahana et al, 2013) or when test results are confidential due to patents (Cole et al, 2016).…”

“…Previous studies have highlighted the importance of large-scale genotyping to validate candidate causal mutations (Schwarzenbacher et al, 2016a,b;Michot et al, 2017;Fritz et al, 2018). Our team recently excluded a candidate variant in the SHBG gene for MH1 haplotype in Montbéliarde cattle (Fritz et al, 2013) and validated a new causal variant in the PFAS gene (Michot et al, 2017).…”

“…To fine map the causal mutation associated with the newly detected NH7 haplotype, we followed the approach used by Sonstegard et al (2013) and Fritz et al (2018). Briefly, this consisted in identifying phenotypically normal animals presenting a run-of-homozygosity (ROH) on either side of the candidate haplotype among the inbred descendant of the bull (Nonnic; NORFRAM002977029292), the most ancient and influential carrier of NH7 in our data set.…”

“…Interestingly, 5 out of the 8 variants were within our fine-mapped critical region, which could include the causal variant. However, it is known from studies that the best candidates do not always have perfect correlation with the causal haplotype (Michot et al, 2017;Fritz et al, 2018), which could be due to various artifacts (e.g., errors in phasing and imputation, errors in sequencing and WGS genotype calls, Figure 3. Identification of putative causal variants within the Normande haplotype NH7 locus (±500 kb) using Pearson correlation between haplotype status and allele dosage of whole-genome sequencing (WGS) variants.…”

“…However, some of these haplotypes could not be confirmed in independent studies, possibly because of falsepositive results or population structure within a breed. For example, haplotypes HH2 in Holstein and BH1 in Brown Swiss showed significant HHD in the United States (VanRaden et al, 2011) but not in Europe (Fritz et al, 2013;Segelke et al, 2016;Fritz et al, 2018). For this reason, and because no phenotypic association and candidate mutation have been reported so far (Mc-Clure et al, 2014), HH2 and BH1 have been recently removed from the list of genetic defects considered by the National Association of Animal Breeders (NAAB) in the United States (Olivier Bulot, World Brown Swiss Federation, Paris, France, personal communication).…”