Diversity Arrays Technology (DArT) for whole-genome profiling of barley

TLDR

DArT can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. The study demonstrates that DArT can be effectively applied to genetic mapping and diversity analyses in barley and validates its Mendelian behavior by constructing a genetic map from a Steptoe × Morex cross. The authors tested multiple complexity‑reduction strategies and chose two that yielded the most polymorphic genomic representations for DArT arrays. The resulting DArT fingerprints achieved a 98.0 % call rate and ≥99.8 % reproducibility, accurately grouped barley lines by known relationships, mapped 98.8 % of polymorphic features into seven linkage groups with ~385 markers spanning 1,137 cM, and matched or exceeded the quality of an RFLP framework map, underscoring DArT’s utility for genome profiling in breeding and genomics.

Abstract

Diversity Arrays Technology (DArT) can detect and type DNA variation at several hundred genomic loci in parallel without relying on sequence information. Here we show that it can be effectively applied to genetic mapping and diversity analyses of barley, a species with a 5,000-Mbp genome. We tested several complexity reduction methods and selected two that generated the most polymorphic genomic representations. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 98.0% and a scoring reproducibility of at least 99.8%. The fingerprints grouped barley lines according to known genetic relationships. To validate the Mendelian behavior of DArT markers, we constructed a genetic map for a cross between cultivars Steptoe and Morex. Nearly all polymorphic array features could be incorporated into one of seven linkage groups (98.8%). The resulting map comprised ≈385 unique DArT markers and spanned 1,137 centimorgans. A comparison with the restriction fragment length polymorphism-based framework map indicated that the quality of the DArT map was equivalent, if not superior, to that of the framework map. These results highlight the potential of DArT as a generic technique for genome profiling in the context of molecular breeding and genomics.