Sequencing and Genotyping in a Complex Genome: Current Status and Future Possibilities

Implementation of marker assisted breeding methods in plant species is expanding at a rapid pace.  Consortia offer groups an opportunity to pool resources to spread the cost of creating genotyping tools over more samples.  This effectively lowers the barrier of entry for single users, breeders, or research scientists to implement a species-specific tool in their lines of interest.  Examples where consortia have been successful include SolCAP species (tomato and potato), RosBREED (apple, peach and cherry), and even in hexaploid species such as wheat. The implementation of genotype calling tools into such a screening or breeding program requires extension of existing reliable, reproducible, automated calling methods in polyploid species. We will provide examples of calling methods that can be employed and the responsibilities of developing a consortium around the development of high density SNP genotyping tools in oat.