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

Janez Jenko, Matthew C. McClure, Daragh Matthews, Jennifer McClure, Martin Johnsson, Gregor Gorjanc, John Hickey*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Background: 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. 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.
Methods: In 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.
Results: We 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.
Conclusions: We 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.
Original languageEnglish
Article number9
Pages (from-to)1-14
Number of pages14
JournalGenetics Selection Evolution
Volume51
Issue number9
DOIs
Publication statusPublished - 5 Mar 2019

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