A comparison of genotypes generated by infinium beadchips and a targeted genotype by sequencing method in cattle — ASN Events
  1. Schedule
  2. Concurrent 15 - Detecting causal variants II
  3. A comparison of genotypes generated by infinium beadchips and a targeted genotype by sequencing method in cattle

A comparison of genotypes generated by infinium beadchips and a targeted genotype by sequencing method in cattle (#87)

Amanda Chamberlain 1 , Phil Beatson 2 , Brett Mason 1 , Claire Prowse-Wilkins 1 , Coralie Reich 1 , Chris Schrooten 3 , Ben Hayes 1 4 , Josquin Tibbits 1 5 , Matthew Hayden 1
  1. Biosciences Research, DEDJTR, Bundoora, VIC, Australia
  2. CRV, Hamilton, New Zealand
  3. CRV, Arnhem, Netherlands
  4. La Trobe University, Bundoora, Australia
  5. University of Melbourne, Parkville, Australia

The cost of SNP genotyping is of major importance in genomic selection programs. One possibility for reducing the expense of applying genomic selection would be to take advantage of recent dramatic decreases in the cost of genome sequencing, by using genotyping-by-sequencing (GBS) techniques to provide cheaper genotypes. This paper presents a GBS method that can target individual variants and therefore any SNP of interest. Comparing array and GBS genotypes from 471 individuals for 5119 SNP we show that with GBS we can achieve sample call rates of 93%, as compared with 95% for arrays, and that genotypes called from the GBS are 98% concordant with those from SNP arrays. With further refinement of the custom reference we will be able to achieve higher call rates and genotyping accuracy.

Full Paper