Evolution of Genotyping in Commercial Plant Breeding.

SNP detection platforms have become the preferred genotyping methods in plant breeding programs because of concomitant productivity gains achievable through assay simplification and automation. What SNPs lack in relative information per marker, they provide in abundance and diagnostic simplicity enabling researchers to reduce costs through automation. Detection choices abound, but need to fulfill the requirements of various breeding applications both in terms of assay x sample flexibility and scale. The increased scale and inevitable automation complexity require additional specialized skills to be available in the laboratory, particularly automation and IT capabilities. As markers become a routine part of the breeding process, increased specialization of platforms for specific applications occurs as the assay x sample matrix continues to extend and speed becomes more paramount. Finally, with the phenomenal advances in sequencing the line between genotyping and whole genome sequencing continues to blur with the promise that sequencing could someday become a routine part of the breeding process. The evolution of genotyping platforms in the environment of a commercial plant breeding program and the impact of new technologies will be discussed.