Whole genome association mapping in barley: constraints and opportunities

Conventional crop plant breeding essentially rests on repeated cycles of crossing and selection. This approach has warranted the development of superior cultivars over the past decades. However, this approach is only sustainable, if the genetic diversity that is lost in the process of selection is adequately replenished by introducing novel diversity into the genepool. Ex-situ conservation of plant genetic resources represents the major backbone to maintain the intraspecific diversity of many important crop plant species. By the turn of the century than 6 million seed samples were stored in more than 1000 ex-situ collections worldwide.  However, the vast diversity resting on the shelves of genebanks has been tapped into only marginally.  The availability of an ever increasing amount of sequence information has greatly spurred the development of a comprehensive set of SNP markers. These now allow for high density fingerprinting of large number of individuals and the genetic analysis of quantitative traits by QTL analysis or association mapping. Moreover, the systematic exploitation of intergenomic information will accelerate the isolation of traits by map based cloning, even in complex genomes such as that of barley. The ultimate goal to fully exploit the potential of molecular breeding will be the generation of a high quality genomic sequence of barley which is presently underway. Knowledge of the genes that underlie agronomic traits will allow to systematically sifting through genebank collections for the identification novel alleles.