Journal Article

Genetic and genomic testing of cattle from tissue sample units under Australian conditions

Lyons, R E, Waine, D, Lyons, K, Frost, L, Kelly, M, Collis, E

2016

Overview

The increasing integration of livestock production systems of Australia and elsewhere, including the implementation of traceability programs such as the National Livestock Identification System (NLIS), means that animals are tagged early in life. These programs must accommodate a range of production systems, including those extensive operations where the animal may be handled only sporadically for weaning or other husbandly. With the increased use of genetic and genomic technologies for research and as decision making tools in selective breeding programs, these occasions are being seen as an opportunity to sample animals for genetic testing, including parentage analysis, disease diagnostics, and more recently genomics for use in estimating genetic estimated breeding values. Sample types commonly include hair, blood, semen, and most recently tissues collected during the tagging process. Tissue sampling units (TSU) are now marketed by a range of companies as a convenient way to collect tissue for DNA in parallel with tagging, providing benefits, which include labor reduction, trace-ability, and reduced risk of transcription errors. These TSUs commonly come with or without preservative, with the dry type being used to great effect in Europe and New Zealand. However, dry TSUs have proven problematic under Australian conditions. Transit times for postage under hot and often humid conditions often lead to rapid deterioration of the tissue, such that DNA quality is compromised and testing impossible. To optimize the collection of workable samples for industry, heat challenges were performed that confirmed the superiority of preservative-filled TSUs for genetic testing. These preservative-filled TSUs were further evaluated for tissue stability and quality of DNA extracted for a range of genetic and genomic tests performed in the laboratory, including microsatellite-and SNP-based parentage testing, diagnostics, and genomic applications using SNP genotyping microarray teclinology. An important research question of this study was also how best to maintain (biobank) tissue or DNA in a cost-effective manner for testing in the future. The current study potentially has insights for future application in studies across a range of tropical and sub-tropical climates.

• Publisher: Oxford University Press
• Subject: Animals / Breeding / Cattle / Decision making / Deoxyribonucleic acid / DNA / DNA microarrays / Genetic analysis / Genetic screening / Genetic testing / Genomics / Genotyping / Livestock / Livestock production / Marking / Preservatives / Selective breeding / Semen / Single-nucleotide polymorphism / Software / Stability analysis / Tagging / Tissues / Transcription / Travel time / Weaning