The GDR Is a Critical Resource for Developing and Refining Trait-Predictive DNA Tests

DNA tests for traits of interest for genetic crop improvement are a key need for translating genomics research outcomes into breeding practice. DNA tests (trait-predictive markers) target particular Mendelian or quantitative trait loci (QTLs) to reveal genotypes that predict phenotype. For more than a decade, the Genome Database for Rosaceae (GDR) has streamlined DNA test development and refinement for rosaceous crops. Typically, a researcher wanting to develop a new DNA test starts with knowledge of the genomic location of a trait locus of interest and its genotypes for two or more cultivars (such as parents of the QTL discovery mapping population). The GDR is then consulted. For simple PCR-based DNA tests, first, the QTL position is zoomed into (CMap; GBrowse) and nearby DNA sequence obtained (Sequence Retrieval; Download Sequence File). Next, motifs of possible polymorphism are sought and primers are designed to flank them to produce amplicons of desired lengths (Primer3). Primers are checked to ensure they only amplify the target locus (BLAST). Sets of primers representing candidate assays can be commercially procured and then PCR conducted to examine segregation of amplicons and their match to known cultivar genotypes. DNA test primers reported from other research groups can be refined by adding a longer “GC clamp” to enhance annealing (Primer3) and their genomic position checked in the crop's latest genome assembly (BLAST; GBrowse). Comparative mapping can fast-track new DNA tests development, exploiting Rosaceae synteny (Synteny Viewer; RosMAP). Further opportunities beckon to enhance genomics translation into breeding tools and knowledge.