Mapped clone sequences detecting differences among 28 North American barley cultivars

Genetic linkage maps of molecular markers have been developed for barley (Hordeum vulgare L.) to aid development of improved barley cultivars. However, crosses between genetically diverse parents used to maximize polymorphism in map construction are not appropriate for use in breeding programs for cultivar development. The objective of this study was to determine whether the amount of genetic variation detected at RFLP (restriction fragment length polymorphism) marker loci among 28 North American spring barley cultivars was sufficient to permit molecular marker-assisted selection in North American barley breeding programs. DNA extracted from these cultivars was restriction digested with BamHI and hybridized to 100 clone sequences mapped by the North American Barley Genome Mapping Project. A diversity index (DI) was calculated for each clone sequence based on the number and frequency of RFLP patterns detected. Fifty-seven of the clones detected RFLPs among these cultivars. Twenty-nine of these were highly informative (DI>0.500) in detecting differences among the 28 cultivars. Clone sequences were identified that separated the 28 cultivars by geographic origin (Western vs. Midwestern) and by spike morphology (two-rowed vs. six-rowed. While 47% of the clone sequences detected RFLPs among the 15 Midwestern six-rowed cultivars, only 17% detected RFLPs among the currently grown cultivars Robust, Excel, Foster, and Stander. The RFLP loci that differ between these cultivars appear to be associated with quantitative trait Loci (QTL) for agronomic and malt quality traits. Molecular marker-assisted selection in malting barley breeding programs can be used to select the optimal alleles at these QTL and to incorporate qualitative traits such as disease resistance from less adapted germplasm.