The North American Collaborative Oat Research Enterprise (CORE)
Genomics and Gene Discovery
2012 Annual Report
1a.Objectives (from AD-416):
Bioinformatics and database support for the CORE project is being tasked to house and analyze data for the North American effort to improve information related to oat germplasm based on sequencing, molecular marker information, and analysis of trait diversity.
1b.Approach (from AD-416):
A germinal set of molecular marker information created for the CORE collection has been created using modern sequencing technologies and has been used to build genetic maps in several oat mapping populations. Annotations are being created to identify key traits in oat and to test molecular markers to track down and validate candidate trait identities. Resources for these analyses are being placed in relational databases by GGD personnel which is made available to CORE project members and collaborators.
Using sequence data from twenty oat germplasm lines, a collection of single nucleotide polymorphism (SNP) markers has been prepared. Based on two successful rounds of probe design, chip creation, and screening on the Illumina GoldenGate assay system, another set of probes was created for the Illumina Infinium assay system. The latest chip design is a culmination of marker data derived from DArT, Roche 454, and Illumina sequence data. Enhancements were made to the SNP selection protocol, and the performance of new markers based on the Illumina genotyping-by-sequencing approach is currently under evaluation. Initial phase SNP markers have been thoroughly tested on six mapping populations, and a consensus map comprising 21 linkage groups representing the 21 chromosomes of hexaploid oat has been generated. Early data was placed into a database based on The Hordeum Toolkit (THT) and termed The Avena Toolkit (TAT). Subsequently a different database system based on a content management system (CMS) was adopted, currently being developed as The Oat Tool Environment (TOTE). A manuscript reporting this work is currently under review. Plans are to interface the new SNP markers with genotype and phenotype data being collected for the Coordinated Oat Research Enterprise (CORE) project effort. This research is contributing to parent project Sub-objective 1.A., "Integrate genetic and physical maps of small grains with developing genomic sequences and link to rice and Brachypodium model genomes".