Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize

The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample the genetic diversity. Genotyping-by-sequencing has become a widely adopted method for cost-effective genotyping. It basically requires no initial investment for design as compared to array-based platforms which have shown to offer very robust assays. The latter, however, poses the drawback of being bound to the genetic diversity accounted during the selection and design. On the contrary, genotyping-by-sequencing with random sampling of genomic loci via restriction enzymes or random priming has shown to be fast and convenient but lacks the ability to target specific regions of the genome and to maintain high reproducibility across laboratories.