Ways to Unlock Barley´s Secondary Gene Pool for Breeding By Next-Generation-Sequencing

Crop wild relatives (CWR) have been recognized as a source of beneficial traits to a given crop species and to overcome the erosion of genetic diversity resulting from domestication and small effective population size in elite breeding programs. The efficient utilization of crop-wild introgression lines for improving elite germplasm has largely been hampered due to the lack of suitable molecular tools for locating introgressed segments and decreasing their size during subsequent crosses. Marker development in CWR is mainly restricted by limited access to the genomic information of these species. We explored the usefulness of Next-Generation-Sequencing technology for developing and scoring molecular markers in a diploid introgression line of cultivated barley (Hordeum vulgare L.) containing chromatin from its wild relative Hordeum bulbosum L.. We used a recently developed whole exome capture assay in combination with a custom SNP genotyping assay as well as two-enzyme genotyping-by-sequencing to allocate the introgression interval and to genotype progeny segregating for the introgression. Both methods provided fast and reliable detection and mapping of the introgressed segment and enabled the identification of recombinant plants avoiding tedious and iterative steps of marker development. Furthermore, the study suggests that the same tools may be applied to high density genotyping and mapping of segregating populations of H. bulbosum and even more distantly related Hordeum species. This will ultimately pave the way for detailed comparative genomics within the genus Hordeum.