Oat improvement - in silico

Abstract

Oat improvement is driven by information and ideas. Broadly speaking, bioinformatics is a field dedicated to the exchange and interpretation of information. The purpose of this study was to describe and evaluate various bioinformatics tools (programs and databases) based on their relevance to oat improvement. An inventory of bioinformatics tools was developed, and these were described and evaluated based on their relevance to a traditional cycle of oat improvement. This inventory includes tools developed by the authors, as well as many other tools that are freely available on the Internet. The primary components of the traditional oat improvement cycle include (1) Parent selection and population development, (2) germplasm selection, and (3) variety evaluation. Tools associated with parent selection include germplasm databases, a newly developed oat pedigree database, databases containing results of screening tests, and databases of marker allele surveys. We report a new tool, Gelato , for building and maintaining inventories of marker surveys. Tools associated with variety screening are the most numerous, since these include all tools related to molecular marker development and QTL association. We report a new database that allows simple and systematic queries of QTLs identified in oat. Tools associated with variety evaluation include databases that can facilitate detailed studies of cultivar adaptation and end-use quality. We report a new database and query tool that can facilitate assimilation and data mining of multi-trait, multi-environment variety trials. References: Links to databases described in this study are maintained at: http://gnomad.agr.ca/oat/