McClure, M. C. | bioRxiv Science

bioRxiv2018

Analysis of a large data set reveals haplotypes carrying putatively recessive lethal alleles with pleiotropic effects on economically important traits in beef cattle

BackgroundDeleterious 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.\n\nMethodsIn 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.\n\nResultsWe 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 {euro}3.23, {euro}1.47, and {euro}2.30 for the terminal index and -{euro}3.15, -{euro}0.75, and {euro}1.12 for the replacement index, where one standard deviations are {euro}18.32, {euro}22.54, and {euro}22.33 for terminal index and {euro}29.52, {euro}35.62, and {euro}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.\n\nConclusionsWe 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.

genetics↗

bioRxiv2017

SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification

A major use of genetic data is parentage verification and identification as inaccurate pedigrees negatively affect genetic gain. Since 2012 the international standard for single nucleotide polymorphism (SNP) based verification in Bos taurus cattle has been the ISAG 100 and 200 SNP panels. While these SNP sets have provided an increased level of parentage accuracy over microsatellite markers (MS), they can validate the wrong parent for an animal at [≤]1% misconcordance rate levels, indicating that more SNP are needed if a more accurate pedigree is required. With rapidly increasing numbers of cattle being genotyped in Ireland that represent 61 Bos taurus breeds from a wide range of farm types: beef/dairy, AI/pedigree/commercial, purebred/crossbred, and large to small herd size the Irish Cattle Breeding Federation (ICBF) analysed different SNP densities to determine that at a minimum [≥]500 SNP are needed to consistently predict only one set of parents at a [≤]1% misconcordance rate. For parentage validation and prediction ICBF uses 800 SNP selected based on SNP clustering quality, ISAG200 inclusion, call rate (CR), and minor allele frequency (MAF) in the Irish cattle population. Large datasets require sample and SNP quality control (QC). Most publications only deal with SNP QC via CR, MAF, parent-progeny conflicts, and Hardy-Weinberg deviation, but not sample QC. We report here a genomic sample QC pipeline to deal with the unique challenges of >1,000,000 genotypes from a national herd such as SNP genotype errors from mis-tagging of animals, lab errors, farm errors, and multiple other issues that can arise.

genetics↗