Association Mapping of Agronomic and Quality Traits in a Breeding Population of Hybrid Rye

Rye (Secale cereale L.) is known to be the most drought tolerant cereal adapted to light soils with low water capacity. Rye is established as a renewable resource to supplement and mix up biomass crop rotations without competition in acreages used for food and feed. Model calculations on the global climate change indicate that the main growing areas of rye in Germany will be significantly affected by a decreasing summer rainfall as well as rising temperatures. Thus, rye will be particularly affected by drought stress and novel approaches are needed to enhance the yield potential of rye under changing environmental conditions. Currently, only limited information on markers in linkage disequilibrium (LD) with quantitative trait loci (QTL) is available for this traditional cereal, which could be used to promote selection gain. In this study, we have exploited the genome-wide LD in the allogamous rye as well as the potential of whole genome profiling in a breeding population of hybrid rye using Diversity Arrays Technology (DArT) markers to identify molecular markers for complex inherited traits including grain yield. The overall LD decay was less than 2.5 cM with only few blocks of higher LD on individual chromosomes. Sequence information on markers associated with agronomic and quality traits enabled a comparative genetic approach of QTL mapping between rye and rice. The discovered markers open new perspectives for the characterization and validation of QTL alleles and contribute to strengthen the efficiency of hybrid rye breeding via marker-assisted selection for superior QTL alleles.