Analysis of a Large Dataset Reveals Haplotypes Carrying Putatively Recessive Lethal and Semi-Lethal Alleles with Pleiotropic Effects on Economically Important Traits in Beef Cattle.

Background Deleterious recessive alleles can result in reduced economic performance in livestock in multiple ways in homozygous individuals: from early embryonic death, death soon after birth, to being non-lethal but causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify. However, it can sometimes be observed as reduced artificial insemination (AI) conception rates, longer calving intervals, or higher hazard for live born animals. Methods In this paper, we searched for haplotypes carrying putatively recessive lethal alleles in 132,725 genotyped Irish beef cattle from five breeds: Aberdeen Angus, Charolais, Hereford, Limousin, and Simmental. We phased the genotypes in sliding windows along the genome and used five tests to identify haplotypes with absence of or reduced homozygosity. We then corroborated the identified haplotypes with reproduction records, indicating early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on national estimates of breeding values for 15 economically important traits in beef production. Results We found support for three haplotypes with carrying putatively recessive lethal alleles. The haplotypes were located on chromosome 14 in Aberdeen Angus, chromosome 19 in Charolais and chromosome 16 in Simmental. Their population frequencies is 15.2%, 14.4%, and 8.8%, respectively. All of the haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €3.23, €1.47, and €2.30 for the terminal index and -€3.15, -€0.75, and €1.12 for the replacement index, where one standard deviations are €18.32, €22.54, and €22.33 for terminal index and €29.52, €35.62, and €30.97 for the replacement index. We identified ZFAT as the candidate gene for lethality in Aberdeen Angus, several candidate genes for the Simmental haplotype, and no candidate genes for the Charolais haplotype. Conclusions We analysed genotype, reproduction, survival, and production data to discover haplotypes carrying putatively recessive lethal alleles in Irish beef cattle. We found support for three haplotypes. All three haplotypes have pleiotropic effects on economically important traits in beef production.