Abstract
BackgroundIn livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance 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 conception rates, longer calving intervals, or lower survival for live born animals.MethodsIn this paper, we searched for haplotypes that carry putatively recessive lethal or semi-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. Then, we associated the identified haplotypes with 44,351 insemination records that indicated early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on estimates of breeding value for 15 economically important traits in beef production.ResultsWe found support for one haplotype that carries a putatively recessive lethal (chromosome 16 in Simmental) and two haplotypes that carry semi-lethal alleles (chromosome 14 in Aberdeen Angus and chromosome 19 in Charolais), with population frequencies of 8.8, 15.2, and 14.4%, respectively. These three haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €2.30, €3.42, and €1.47 for the terminal index and €1.03, − €3.11, and − €0.88 for the replacement index, where the standard deviations for the terminal index are €22.52, €18.65, and €22.70 and for the replacement index they are €31.35, €29.82, and €35.79. We identified ZFAT as the candidate gene for semi-lethality in Aberdeen Angus, several candidate genes for the lethal Simmental haplotype, and no candidate genes for the semi-lethal Charolais haplotype.ConclusionsWe analysed genotype, reproduction, survival, and production data to detect haplotypes that carry putatively recessive lethal or semi-lethal alleles in Irish beef cattle and identified one lethal and two semi-lethal haplotypes, which have pleiotropic effects on economically important traits in beef production.
Highlights
In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability
Our results identified one haplotype that carries a putatively recessive lethal allele and two haplotypes that carry putatively recessive semi-lethal alleles, which were located on chromosome 16 in Simmental, chromosome 14 in Aberdeen Angus, and chromosome 19 in Charolais, respectively
We identified the zinc finger and AT-hook domain containing (ZFAT) gene as the potential causative gene for semilethality in Aberdeen Angus
Summary
Deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify It can sometimes be observed as reduced conception rates, longer calving intervals, or lower survival for live born animals. Recessive lethal alleles are one of the genetic causes of reproduction inefficiency, because they result in embryonic death when an embryo is homozygous They can reduce viability of embryos and liveborn animals when their effect is not fully expressed (incomplete penetrance). In some cases, it is observed as reduced conception rates, longer calving intervals, or lower survival for live born animals Such alleles tend to be rare, but if their frequency increases, the number of affected (homozygous) embryos increases and so does the economic loss. This would lead to the selection of heterozygous carriers as parents of the generation, propagate the recessive lethal allele across the population, and in turn significantly affect reproduction [17]
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