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 acquired 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.
Genotyping by Sequencing
Second Generation Sequencing (2GS) has recently opened up opportunities to develop very high-throughput genotyping assays. We are currently developing and optimising Genotyping by Sequencing (GbS) assays in cereal and soft fruit species which will enable extremely cost-effective diversity analysis and high-density genetic mapping. Please contact Pete Hedley or Hui Liu for further information.
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