Genotyping
In order to determine the genetic basis for the phenotypic traits of an organism, it is essential to identify the underlying genotype. Although low throughput assays such as Simple Sequence Repeats (SSRs) continue to be used and processed at The James Hutton Institute, the use of Single Nucleotide Polymorphisms (SNPs) enable transition to high-throughput multiplexing.
Illumina genotyping
Within the Genome Technology lab we have a BeadXpress (Illumina) system which utilises GoldenGate technology for medium-throughput SNP genotyping. Custom assays have been designed for several plant species including barley, Lolium and soft fruit, in either 384- or 96-plex format. These designs have primarily been derived from 2GS RNA-seq data sets. The group processes 5,000 samples per annum, equating to 2 million datapoints. For further details, please contact Pete Hedley or Malcolm Macaulay.
Sequencing-based genotyping
Second Generation Sequencing (2GS) has recently opened up opportunities to develop very high-throughput genotyping assays. We have developed and optimised Genotyping by Sequencing (GbS) assays in cereal and soft fruit species which enable extremely cost-effective diversity analysis and high-density genetic mapping. In addition, the recent acquisition of an Illumina MiSeq platform in the group has led to conversion of GoldenGate SNP assays into sequencing-based markers. this has been done in collaboration with Eureka Genomics in the US (http://www.eurekagenomics.com/ws/home.html). Please contact Pete Hedley for further information.
