Sequencing & Pangenomes

Optimization of a custom ThermoFisher Applied Biosystemsà¢â€žÂ¢ Axiomà¢â€žÂ¢ genotyping array for Irish beef and dairy cattle

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Abstract

The Irish Cattle Breeding Federation (ICBF) database holds over 6.2m genotypes, 6m of which emanate from versions of the custom ICBF genotyping array, the 'International Dairy and Beef' (IDB). The IDB SNP array was developed in 2013 by ICBF in collaboration with industry partners. The content and performance of the array is under periodic review, with multiple iterations since developed. The design of the IDB version 6, a ThermoFisher Applied Biosystemsâ„¢ Axiomâ„¢ Genotyping array first involved a performance review of existing array content (n=51,421 SNPs) which was evaluated using genotype data from previous IDB iterations in the ICBF database. This included SNP call rate and allele frequency based on 2.1m genotypes and ThermoFisher Applied Biosystemsâ„¢ Axiomâ„¢ SNP classification data based on ~630k genotypes. New markers included 140 additional genetic traits identified via the Online Mendelian Inheritance in Animals (OMIA) compendium, 2.8k genome wide markers for genetic evaluation purposes and ~350 research markers. The final design consisted of 148,408 probes targeting 56,059 unique markers including an updated ICBF 800 parentage SNP panel which includes the International Committee for Animal Recording (ICAR) 554 SNPs for parentage discovery, genome wide markers for genomic evaluation and research purposes, X and Y markers for gender prediction, and 206 genetic traits e.g. Myostatin, Polled. Coordinates were aligned to Bos taurus genome version ARS-UCD1.2 and Y chromosome markers were aligned to Btau5.0.1.The validation design included 2 x 384 format arrays. High quality DNA samples were identified using genotypes in the ICBF database to represent variables such as sample type (ear tissue - Allflex, Caisley, and Datamars tags, hair, semen, BVD and milk), breed, sex, farm, and genetic trait status. Samples were genotyped at both ICBF service provider laboratories using the High-Level Axiom Propel XPRES 384HT Workflow followed by analysis using the Best Practices Genotyping Analysis Workflow. Genotype concordance analysis, which was carried out in house, evaluated both service provider performance and assessed concordance within marker panels such as genotype imputation, parentage, sex prediction, microsatellite imputation, and the IDBv3 component. Carriers for genetic traits including those routinely reported to industry via the ICBF major gene pipeline were also reviewed. Other metrics assessed were sample type performance, allele orientation, file formats and presence of expected content. The concordance analysis indicated comparable performance to IDBv5; on average, concordance across marker panels was 99.5%. Following finalization of marker content (n=55,063), development of SNP specific prior (SSPs), allele orientation changes, and library file settings, the IDBv6 was implemented in Autumn 2024. Of 1.3 million IDBv6 genotypes now available, 99.2% have a sample call rate of >=90% while 99% of markers have a call rate of >=90%. This project validates the IDBv6 microarray as a high-performance genotyping platform for Irish cattle.

Keywords: 2026

How to Cite:

Quigley, K., Browne, T., O’ Connell, K., Evans, R. & Mullen, M., (2026) “Optimization of a custom ThermoFisher Applied Biosystemsà¢â€žÂ¢ Axiomà¢â€žÂ¢ genotyping array for Irish beef and dairy cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285028. doi: https://doi.org/10.31274/wcgalp.23628

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