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Monday, August 6 • 3:00pm - 3:20pm
Management 1 Track: Using Low-Depth Genotyping-by-Sequencing for Genomic Analyses in Farmed New Zealand Deer

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AUTHORS: Suzanne J. Rowe, Ken G. Dodds, Jamie F. Ward, Geoff W. Asher, Tracey van Stijn, Rudiger Brauning, John C. McEwan, Andrew Hess – AgResearch Limited, Invermay Agricultural Centre

ABSTRACT: In New Zealand, there are currently ~1million commercially farmed deer, farmed mainly for venison and for velvet. The New Zealand deer industry uses genomic testing to obtain parentage and pedigrees for the purposes of breeding and selection. Recently, a new direct sequencing method (Elshire et al., 2011) has been applied to New Zealand deer. It involves direct sequencing of DNA from ear punch tissue. The method, genotyping-by-sequencing (GBS) has been used to obtain ~80,000 marker genotypes per animal without the need to develop commercial assays or to have a sequenced genome. The New Zealand deer industry is using GBS for parentage (Dodds et al., 2018) as deer behaviour prohibits intensive management of hinds, but these genotypes also offer new opportunities to harness genomic information. The purpose of this study was to explore further utility for the genotypes generated for parentage. Here we use over 1,000 recorded deer to show use of the method for parentage verification, breed/species assignment, finding major genes using genome-wide association studies (GWAS), and genomic prediction in New Zealand deer. Challenges of using this method involve handling sequence data of varying depth within a commercial platform to estimate genomic relationships (Dodds et al., 2015). Advantages include tens of thousands of markers at a price point equivalent to parentage. Accuracies for genomic prediction of commercial farm traits were assessed. Quantitative trait loci were identified for yearling weight and a candidate gene was proposed. An added challenge for genomic prediction in deer is the presence of two distinct species and the use of cross-breds. To address this, we adjusted genomic relationships based on the underlying marker allele frequencies in each species (Hess et al., 2018). This tool was developed for commercial parentage and breeding but has potential for many uses including population and conservation genetics.

467591 pdf
3pm pdf

Monday August 6, 2018 3:00pm - 3:20pm
Assembly Hall A
  • Slides Available Yes

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